[Swift-commit] r5984 - in SwiftApps/CMTS/stringmethod: . bin src src/data
davidk at ci.uchicago.edu
davidk at ci.uchicago.edu
Mon Oct 22 09:57:21 CDT 2012
Author: davidk
Date: 2012-10-22 09:57:20 -0500 (Mon, 22 Oct 2012)
New Revision: 5984
Added:
SwiftApps/CMTS/stringmethod/bin/
SwiftApps/CMTS/stringmethod/bin/stringmethod
SwiftApps/CMTS/stringmethod/src/
SwiftApps/CMTS/stringmethod/src/EN_BOLTZMANN_MIXING_INFO
SwiftApps/CMTS/stringmethod/src/EN_BOLTZMANN_MIXING_INFO_2
SwiftApps/CMTS/stringmethod/src/INPUT_STRUCTURE_1
SwiftApps/CMTS/stringmethod/src/INPUT_STRUCTURE_2
SwiftApps/CMTS/stringmethod/src/INPUT_STRUCTURE_2_1
SwiftApps/CMTS/stringmethod/src/INPUT_STRUCTURE_2_2
SwiftApps/CMTS/stringmethod/src/INPUT_STRUCTURE_b_1
SwiftApps/CMTS/stringmethod/src/INPUT_STRUCTURE_b_2
SwiftApps/CMTS/stringmethod/src/LANGEVIN_FRICTION
SwiftApps/CMTS/stringmethod/src/LANGEVIN_FRICTION_2
SwiftApps/CMTS/stringmethod/src/MASSES_PARTICLES
SwiftApps/CMTS/stringmethod/src/MASSES_PARTICLES_2
SwiftApps/CMTS/stringmethod/src/Makefile
SwiftApps/CMTS/stringmethod/src/README
SwiftApps/CMTS/stringmethod/src/README_FOR_INPUT_FILE_FORMATS
SwiftApps/CMTS/stringmethod/src/RESIDUE_NAMES
SwiftApps/CMTS/stringmethod/src/RESIDUE_NAMES_2
SwiftApps/CMTS/stringmethod/src/SIMULPARAMS_NAMD_UNIT
SwiftApps/CMTS/stringmethod/src/calc_rmsd_from_one_structure.c
SwiftApps/CMTS/stringmethod/src/calc_rmsd_from_one_structure.h
SwiftApps/CMTS/stringmethod/src/common_functions.c
SwiftApps/CMTS/stringmethod/src/common_functions.h
SwiftApps/CMTS/stringmethod/src/data/
SwiftApps/CMTS/stringmethod/src/data/CONSTRAINS-EXT-EXT
SwiftApps/CMTS/stringmethod/src/data/CONSTRAINS-EXT-EXT_2
SwiftApps/CMTS/stringmethod/src/data/CONSTRAINS-EXT-EXT_2b
SwiftApps/CMTS/stringmethod/src/data/CONSTRAINS-FINE
SwiftApps/CMTS/stringmethod/src/data/Collective_variables
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_0
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_1
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_10
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_11
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_12
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_13
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_14
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_15
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_16
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_17
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_18
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_19
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_20
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_21
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_22
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_23
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_24
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_25
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_26
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_27
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_28
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_29
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_0
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_1
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_10
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_11
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_12
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_13
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_14
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_15
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_16
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_17
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_18
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_19
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_2
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_20
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_21
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_22
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_23
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_24
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_25
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_26
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_27
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_28
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_29
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_3
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_30
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_31
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_4
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_5
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_6
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_7
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_8
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_9
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_3
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_30
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_31
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_4
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_5
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_6
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_7
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_8
SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_9
SwiftApps/CMTS/stringmethod/src/data/elastic-network-potential-energy
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_0.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_1.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_10.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_11.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_12.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_13.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_14.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_15.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_16.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_17.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_18.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_19.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_20.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_21.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_22.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_23.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_24.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_25.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_26.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_27.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_28.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_29.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_0.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_1.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_10.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_11.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_12.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_13.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_14.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_15.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_16.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_17.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_18.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_19.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_2.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_20.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_21.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_22.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_23.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_24.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_25.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_26.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_27.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_28.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_29.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_3.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_30.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_31.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_4.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_5.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_6.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_7.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_8.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_9.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_3.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_30.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_31.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_4.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_5.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_6.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_7.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_8.pdb
SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_9.pdb
SwiftApps/CMTS/stringmethod/src/data/repulsive-potential-energy
SwiftApps/CMTS/stringmethod/src/data/rmsd_from_structure_1_with_time
SwiftApps/CMTS/stringmethod/src/data/rmsd_from_structure_1b_with_time
SwiftApps/CMTS/stringmethod/src/data/rmsd_from_structure_2_with_time
SwiftApps/CMTS/stringmethod/src/data/rmsd_from_structure_2b_with_time
SwiftApps/CMTS/stringmethod/src/data/track-progress
SwiftApps/CMTS/stringmethod/src/data/trajectory_all_0.pdb
SwiftApps/CMTS/stringmethod/src/data/trajectory_all_1.pdb
SwiftApps/CMTS/stringmethod/src/data/trajectory_all_10.pdb
SwiftApps/CMTS/stringmethod/src/data/trajectory_all_11.pdb
SwiftApps/CMTS/stringmethod/src/data/trajectory_all_12.pdb
SwiftApps/CMTS/stringmethod/src/data/trajectory_all_13.pdb
SwiftApps/CMTS/stringmethod/src/data/trajectory_all_14.pdb
SwiftApps/CMTS/stringmethod/src/data/trajectory_all_15.pdb
SwiftApps/CMTS/stringmethod/src/data/trajectory_all_16.pdb
SwiftApps/CMTS/stringmethod/src/data/trajectory_all_17.pdb
SwiftApps/CMTS/stringmethod/src/data/trajectory_all_18.pdb
SwiftApps/CMTS/stringmethod/src/data/trajectory_all_19.pdb
SwiftApps/CMTS/stringmethod/src/data/trajectory_all_2.pdb
SwiftApps/CMTS/stringmethod/src/data/trajectory_all_20.pdb
SwiftApps/CMTS/stringmethod/src/data/trajectory_all_21.pdb
SwiftApps/CMTS/stringmethod/src/data/trajectory_all_22.pdb
SwiftApps/CMTS/stringmethod/src/data/trajectory_all_23.pdb
SwiftApps/CMTS/stringmethod/src/data/trajectory_all_24.pdb
SwiftApps/CMTS/stringmethod/src/data/trajectory_all_25.pdb
SwiftApps/CMTS/stringmethod/src/data/trajectory_all_26.pdb
SwiftApps/CMTS/stringmethod/src/data/trajectory_all_27.pdb
SwiftApps/CMTS/stringmethod/src/data/trajectory_all_28.pdb
SwiftApps/CMTS/stringmethod/src/data/trajectory_all_29.pdb
SwiftApps/CMTS/stringmethod/src/data/trajectory_all_3.pdb
SwiftApps/CMTS/stringmethod/src/data/trajectory_all_30.pdb
SwiftApps/CMTS/stringmethod/src/data/trajectory_all_31.pdb
SwiftApps/CMTS/stringmethod/src/data/trajectory_all_4.pdb
SwiftApps/CMTS/stringmethod/src/data/trajectory_all_5.pdb
SwiftApps/CMTS/stringmethod/src/data/trajectory_all_6.pdb
SwiftApps/CMTS/stringmethod/src/data/trajectory_all_7.pdb
SwiftApps/CMTS/stringmethod/src/data/trajectory_all_8.pdb
SwiftApps/CMTS/stringmethod/src/data/trajectory_all_9.pdb
SwiftApps/CMTS/stringmethod/src/en_boltzmann_mixing_stuff.c
SwiftApps/CMTS/stringmethod/src/en_boltzmann_mixing_stuff.h
SwiftApps/CMTS/stringmethod/src/force_constants_out
SwiftApps/CMTS/stringmethod/src/force_constants_out_2
SwiftApps/CMTS/stringmethod/src/include_all.h
SwiftApps/CMTS/stringmethod/src/integrator_ld_Vanden_Eijnden_Cicotti.c
SwiftApps/CMTS/stringmethod/src/integrator_ld_Vanden_Eijnden_Cicotti.h
SwiftApps/CMTS/stringmethod/src/job_omp-stringmethod.sh
SwiftApps/CMTS/stringmethod/src/kinetic-energies
SwiftApps/CMTS/stringmethod/src/md_ld_common_d_dimension_namd.h
SwiftApps/CMTS/stringmethod/src/out_en_boltzmann_mixing_info
SwiftApps/CMTS/stringmethod/src/out_en_boltzmann_mixing_info_2
SwiftApps/CMTS/stringmethod/src/output.c
SwiftApps/CMTS/stringmethod/src/output.h
SwiftApps/CMTS/stringmethod/src/pair_distances_1
SwiftApps/CMTS/stringmethod/src/pair_distances_2
SwiftApps/CMTS/stringmethod/src/pair_distances_2_1
SwiftApps/CMTS/stringmethod/src/pair_distances_2_2
SwiftApps/CMTS/stringmethod/src/perform_langevin_dynamics.c
SwiftApps/CMTS/stringmethod/src/perform_langevin_dynamics.h
SwiftApps/CMTS/stringmethod/src/potential-energies
SwiftApps/CMTS/stringmethod/src/read_configuration.c
SwiftApps/CMTS/stringmethod/src/read_configuration.h
SwiftApps/CMTS/stringmethod/src/read_langevin_parameters.c
SwiftApps/CMTS/stringmethod/src/read_langevin_parameters.h
SwiftApps/CMTS/stringmethod/src/read_masses_all_particles.c
SwiftApps/CMTS/stringmethod/src/read_masses_all_particles.h
SwiftApps/CMTS/stringmethod/src/read_simulation_parameters.c
SwiftApps/CMTS/stringmethod/src/read_simulation_parameters.h
SwiftApps/CMTS/stringmethod/src/read_velocities.c
SwiftApps/CMTS/stringmethod/src/read_velocities.h
SwiftApps/CMTS/stringmethod/src/stringmethod
SwiftApps/CMTS/stringmethod/src/stringmethod.c
SwiftApps/CMTS/stringmethod/src/total-energies
SwiftApps/CMTS/stringmethod/src/write_CA_PDB_files.c
SwiftApps/CMTS/stringmethod/src/write_CA_PDB_files.h
SwiftApps/CMTS/stringmethod/src/write_pdb_atom_record.c
SwiftApps/CMTS/stringmethod/src/write_pdb_atom_record.h
SwiftApps/CMTS/stringmethod/src/write_velocities.c
SwiftApps/CMTS/stringmethod/src/write_velocities.h
SwiftApps/CMTS/stringmethod/src/wrtie_configuration.c
SwiftApps/CMTS/stringmethod/src/wrtie_configuration.h
Log:
String method source
Added: SwiftApps/CMTS/stringmethod/bin/stringmethod
===================================================================
--- SwiftApps/CMTS/stringmethod/bin/stringmethod (rev 0)
+++ SwiftApps/CMTS/stringmethod/bin/stringmethod 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1 @@
+link ../src/stringmethod
\ No newline at end of file
Property changes on: SwiftApps/CMTS/stringmethod/bin/stringmethod
___________________________________________________________________
Added: svn:special
+ *
Added: SwiftApps/CMTS/stringmethod/src/EN_BOLTZMANN_MIXING_INFO
===================================================================
--- SwiftApps/CMTS/stringmethod/src/EN_BOLTZMANN_MIXING_INFO (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/EN_BOLTZMANN_MIXING_INFO 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,9 @@
+num_c_alpha_atoms 20
+num_input_structures 2
+cutoff_distances 100.0 100.0
+mixing_coefficients 0.015
+sigma_repulsive 2.5
+epsilon_replusive 1.0
+fixed_value_of_force_constant 2.0
+energy_param_for_force_constant 5.0
+energy_difference_from_first_structure 0.0
Added: SwiftApps/CMTS/stringmethod/src/EN_BOLTZMANN_MIXING_INFO_2
===================================================================
--- SwiftApps/CMTS/stringmethod/src/EN_BOLTZMANN_MIXING_INFO_2 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/EN_BOLTZMANN_MIXING_INFO_2 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,9 @@
+num_c_alpha_atoms 38
+num_input_structures 2
+cutoff_distances 100.0 100.0
+mixing_coefficients 0.015
+sigma_repulsive 2.5
+epsilon_replusive 1.0
+fixed_value_of_force_constant 2.0
+energy_param_for_force_constant 5.0
+energy_difference_from_first_structure 0.0
Added: SwiftApps/CMTS/stringmethod/src/INPUT_STRUCTURE_1
===================================================================
--- SwiftApps/CMTS/stringmethod/src/INPUT_STRUCTURE_1 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/INPUT_STRUCTURE_1 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+24.935 11.697 0.436
+28.340 13.256 0.935
+29.123 14.025 -2.704
+31.999 16.506 -2.699
+32.015 16.967 -6.475
+34.982 19.327 -6.711
+33.387 22.736 -6.313
+29.834 21.481 -5.756
+30.055 20.019 -2.275
+26.812 18.293 -1.401
+26.296 17.205 2.195
+22.859 15.582 2.225
+22.152 14.267 5.722
+19.018 12.478 4.488
+16.554 15.342 4.737
+19.115 17.982 5.791
+20.413 19.133 2.437
+23.572 21.099 3.225
+24.845 22.890 0.122
+28.358 24.244 -0.258
Added: SwiftApps/CMTS/stringmethod/src/INPUT_STRUCTURE_2
===================================================================
--- SwiftApps/CMTS/stringmethod/src/INPUT_STRUCTURE_2 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/INPUT_STRUCTURE_2 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+23.995 10.649 -0.175
+22.858 14.041 -1.471
+21.216 16.343 1.066
+20.371 19.788 -0.261
+18.829 22.755 1.360
+18.263 25.539 -1.124
+21.842 26.669 -1.931
+24.721 24.783 -0.203
+24.874 21.245 -1.553
+25.947 18.531 0.857
+27.429 15.299 -0.348
+27.526 13.105 2.677
+29.512 10.243 1.385
+31.082 9.226 4.698
+32.605 12.692 4.962
+30.078 15.596 4.349
+31.466 17.645 1.408
+30.472 21.215 1.304
+29.551 21.547 -2.445
+28.735 24.634 -4.289
Added: SwiftApps/CMTS/stringmethod/src/INPUT_STRUCTURE_2_1
===================================================================
--- SwiftApps/CMTS/stringmethod/src/INPUT_STRUCTURE_2_1 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/INPUT_STRUCTURE_2_1 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
+24.935 11.697 0.436
+23.703 11.958 -0.452
+28.340 13.256 0.935
+29.204 12.767 2.101
+29.123 14.025 -2.704
+28.057 13.797 -3.816
+31.999 16.506 -2.699
+33.135 16.513 -1.676
+32.015 16.967 -6.475
+30.722 16.798 -7.281
+34.982 19.327 -6.711
+33.387 22.736 -6.313
+33.228 23.710 -7.473
+29.834 21.481 -5.756
+28.915 21.113 -6.941
+30.055 20.019 -2.275
+31.050 20.560 -1.260
+26.812 18.293 -1.401
+26.052 17.554 -2.500
+26.296 17.205 2.195
+26.980 18.057 3.273
+22.859 15.582 2.225
+22.174 15.080 0.961
+22.152 14.267 5.722
+22.497 15.062 6.990
+19.018 12.478 4.488
+16.554 15.342 4.737
+15.442 15.389 5.775
+19.115 17.982 5.791
+19.781 17.998 7.184
+20.413 19.133 2.437
+19.458 19.361 1.265
+23.572 21.099 3.225
+24.611 20.708 4.307
+24.845 22.890 0.122
+23.832 23.541 -0.830
+28.358 24.244 -0.258
+29.593 23.621 0.431
Added: SwiftApps/CMTS/stringmethod/src/INPUT_STRUCTURE_2_2
===================================================================
--- SwiftApps/CMTS/stringmethod/src/INPUT_STRUCTURE_2_2 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/INPUT_STRUCTURE_2_2 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
+23.995 10.649 -0.175
+23.076 10.060 0.941
+22.858 14.041 -1.471
+22.421 14.414 -2.842
+21.216 16.343 1.066
+21.218 15.860 2.601
+20.371 19.788 -0.261
+20.086 19.769 -1.777
+18.829 22.755 1.360
+19.436 22.899 2.852
+18.263 25.539 -1.124
+21.842 26.669 -1.931
+22.413 28.026 -1.630
+24.721 24.783 -0.203
+25.116 25.064 1.282
+24.874 21.245 -1.553
+24.990 21.110 -3.085
+25.947 18.531 0.857
+25.459 18.331 2.261
+27.429 15.299 -0.348
+28.210 15.275 -1.718
+27.526 13.105 2.677
+26.388 13.263 3.754
+29.512 10.243 1.385
+30.080 10.502 -0.080
+31.082 9.226 4.698
+32.605 12.692 4.962
+33.963 12.936 4.372
+30.078 15.596 4.349
+29.385 16.398 5.437
+31.466 17.645 1.408
+31.813 17.100 0.070
+30.472 21.215 1.304
+30.693 22.372 2.334
+29.551 21.547 -2.445
+28.884 20.533 -3.471
+28.735 24.634 -4.289
+29.879 25.541 -4.807
Added: SwiftApps/CMTS/stringmethod/src/INPUT_STRUCTURE_b_1
===================================================================
--- SwiftApps/CMTS/stringmethod/src/INPUT_STRUCTURE_b_1 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/INPUT_STRUCTURE_b_1 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+25.019 13.186 -5.011
+23.011 16.125 -3.456
+22.483 15.469 0.301
+20.537 18.796 0.854
+19.974 18.373 4.618
+17.456 21.239 4.854
+19.700 24.127 5.811
+23.049 22.422 5.250
+23.702 22.019 1.617
+26.038 19.010 0.978
+27.237 17.557 -2.264
+28.810 14.118 -2.332
+31.616 13.681 -4.723
+31.099 10.032 -3.688
+32.409 9.978 -0.156
+33.850 13.493 -0.017
+30.953 15.698 1.145
+31.561 19.175 -0.061
+29.577 22.139 1.131
+27.770 23.785 -1.691
Added: SwiftApps/CMTS/stringmethod/src/INPUT_STRUCTURE_b_2
===================================================================
--- SwiftApps/CMTS/stringmethod/src/INPUT_STRUCTURE_b_2 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/INPUT_STRUCTURE_b_2 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+24.354 13.682 -3.743
+23.172 17.338 -4.179
+21.997 16.774 -0.851
+19.412 18.905 0.748
+19.214 18.564 4.550
+15.997 20.100 5.704
+16.517 23.713 4.908
+20.118 23.883 3.679
+21.506 22.283 0.476
+25.006 21.015 -0.140
+26.847 18.360 -2.163
+28.389 14.919 -1.138
+31.130 13.502 -3.394
+32.022 9.924 -2.756
+31.032 9.386 0.897
+33.762 11.643 2.218
+33.747 15.072 0.560
+31.016 17.265 2.143
+31.076 20.325 -0.073
+29.459 23.465 1.648
Added: SwiftApps/CMTS/stringmethod/src/LANGEVIN_FRICTION
===================================================================
--- SwiftApps/CMTS/stringmethod/src/LANGEVIN_FRICTION (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/LANGEVIN_FRICTION 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,21 @@
+num_particles 20
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
Added: SwiftApps/CMTS/stringmethod/src/LANGEVIN_FRICTION_2
===================================================================
--- SwiftApps/CMTS/stringmethod/src/LANGEVIN_FRICTION_2 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/LANGEVIN_FRICTION_2 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,39 @@
+num_particles 38
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
+0.03
Added: SwiftApps/CMTS/stringmethod/src/MASSES_PARTICLES
===================================================================
--- SwiftApps/CMTS/stringmethod/src/MASSES_PARTICLES (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/MASSES_PARTICLES 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,21 @@
+num_particles 20
+100
+100
+100
+100
+100
+100
+100
+100
+100
+100
+100
+100
+100
+100
+100
+100
+100
+100
+100
+100
Added: SwiftApps/CMTS/stringmethod/src/MASSES_PARTICLES_2
===================================================================
--- SwiftApps/CMTS/stringmethod/src/MASSES_PARTICLES_2 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/MASSES_PARTICLES_2 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,39 @@
+num_particles 38
+50
+50
+50
+50
+50
+50
+50
+50
+50
+50
+50
+50
+50
+50
+50
+50
+50
+50
+50
+50
+50
+50
+50
+50
+50
+50
+50
+50
+50
+50
+50
+50
+50
+50
+50
+50
+50
+50
Added: SwiftApps/CMTS/stringmethod/src/Makefile
===================================================================
--- SwiftApps/CMTS/stringmethod/src/Makefile (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/Makefile 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,49 @@
+
+CC = gcc
+CFLAGS = -fopenmp -Wall -O2 -O3
+LDFLAGS = -lm -fopenmp
+
+
+PROG = stringmethod
+HDRS = calc_rmsd_from_one_structure.h common_functions.h en_boltzmann_mixing_stuff.h include_all.h integrator_ld_Vanden_Eijnden_Cicotti.h md_ld_common_d_dimension_namd.h output.h perform_langevin_dynamics.h read_configuration.h read_langevin_parameters.h read_masses_all_particles.h read_simulation_parameters.h read_velocities.h write_CA_PDB_files.h write_pdb_atom_record.h write_velocities.h wrtie_configuration.h
+SRCS = stringmethod.c calc_rmsd_from_one_structure.c common_functions.c en_boltzmann_mixing_stuff.c integrator_ld_Vanden_Eijnden_Cicotti.c output.c perform_langevin_dynamics.c read_configuration.c read_langevin_parameters.c read_masses_all_particles.c read_simulation_parameters.c read_velocities.c write_CA_PDB_files.c write_pdb_atom_record.c write_velocities.c wrtie_configuration.c
+
+
+OBJS = $(SRCS:.c=.o)
+
+
+#Build the executable
+$(PROG) : $(OBJS)
+ $(CC) $(OBJS) $(LDFLAGS) -o $(PROG)
+
+calc_rmsd_from_one_structure.o : calc_rmsd_from_one_structure.h
+
+common_functions.o : common_functions.h
+
+en_boltzmann_mixing_stuff.o : en_boltzmann_mixing_stuff.h
+
+integrator_ld_Vanden_Eijnden_Cicotti.o : integrator_ld_Vanden_Eijnden_Cicotti.h
+
+output.o : output.h
+
+perform_langevin_dynamics.o : perform_langevin_dynamics.h
+
+read_configuration.o : read_configuration.h
+
+read_langevin_parameters.o : read_langevin_parameters.h
+
+read_masses_all_particles.o : read_masses_all_particles.h
+
+read_simulation_parameters.o : read_simulation_parameters.h
+
+read_velocities.o : read_velocities.h
+
+write_CA_PDB_files.o : write_CA_PDB_files.h
+
+write_pdb_atom_record.o : write_pdb_atom_record.h
+
+write_velocities.o : write_velocities.h
+
+wrtie_configuration.o : wrtie_configuration.h
+
+stringmethod.o : include_all.h
Added: SwiftApps/CMTS/stringmethod/src/README
===================================================================
--- SwiftApps/CMTS/stringmethod/src/README (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/README 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,2 @@
+fine grain: CA+CB
+coarse grain: CA
Added: SwiftApps/CMTS/stringmethod/src/README_FOR_INPUT_FILE_FORMATS
===================================================================
--- SwiftApps/CMTS/stringmethod/src/README_FOR_INPUT_FILE_FORMATS (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/README_FOR_INPUT_FILE_FORMATS 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,64 @@
+/*
+ * Input file name: EN_BOLTZMANN_MIXING_INFO
+ * Format:
+ * NUM_C_ALPHA_ATOMS (%d number of C-alpha atoms)
+ * NUM_INPUT_STRUCTURES (%d number of input structures i.e. number of states)
+ * CUTOFF_DISTANCES (cutoff distances for each structure, separated by white space. Number of cutoffs should be equal
+ * to number of strcutures)
+ * MIXING_COEFFICIENTS (Mixing coeficients for mixing potentials for various structures. Number of coefficients
+ * should be one less than the number of structures. Values should be separated by white space)
+ * SIGMA_REPULSIVE (%lf sigma for the repulsive part of the potential. Same sigma is used for all pairs)
+ * EPSILON_REPULSIVE (%lf epsilon for the repulsive part of the potential)
+ * FIXED_VALUE_OF_FORCE_CONSANT (%lf. Fixed value of force constnat. This value is used unless a different
+ * site dependent value is required to minimize strain. See Albert pan's
+ * string apper JPCB 112, 3432 (2008).)
+ * ENERGY_PARAM_FOR_FORCE_CONSTANT (%lf Energy parameter for site dependent force constant. See the above paper.)
+ * ENERGY_DIFFERENCE_FROM_FIRST_STRUCTURE (%lf Energy difference between the two input structures)
+ * */
+
+
+/*
+ * Input structures should be named as 'input_structure_1', 'input_structure_2',...
+ -------------------
+ Format:
+ * Each line should have x, y, and z cooridnates of one particle (C_ALPHA) separated by white space.
+ * Number of lines should be equal to the number of particles.
+ */
+
+
+/*
+ For Langevin friction.
+ The filename is : LANGEVIN_FRICTION
+ Format:
+ NUM_PARTICLES (number of particles %d)
+ Value of friction coefficients. One value per line (in the unit of fs^{-1})
+*/
+
+
+/* For masses.
+ * 'MASSES_PARTICLES'
+ * Format:
+ * NUM_PARTICLES (number of particles %d)
+ * Masses of particles one per line.
+ * */
+
+
+/*For simulation parameters.
+ The filename is : SIMULPARAMS_NAMD_UNIT
+ Format:
+ RUN_LENGTH_TIME_STEPS (run length in time steps %d)
+ TIMESTEP (timestep in fs %lf)
+ COLLISION_FREQUENCY_TIMESTEP (frequency of thermalizing collisions in timestep %d)
+ TEMPERATURE (temperature in kelvin %lf)
+ CONFIG_SAVE_FREQUENCY (frequency of saving configuration to disk in timestep unit %d)
+ PROGRESS_FREQUENCY (frequency for writing the information about the progress of the calculation in timestep %d)
+ WRITE_FREQUENCY_OTHER (frequency for writing other stuff like kinetic energy, potential energy etc. in timestep unit %d)
+*/
+
+
+/*Input configuration for dynamics*/
+/*
+ Filename: 'INITIAL_CONFIG_C_ALPHA'
+ Format:
+ Each line should have three numbers separated by white space giving x, y, and z cooridnates of one atom.
+ */
Added: SwiftApps/CMTS/stringmethod/src/RESIDUE_NAMES
===================================================================
--- SwiftApps/CMTS/stringmethod/src/RESIDUE_NAMES (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/RESIDUE_NAMES 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+THR
+TRP
+ILE
+GLN
+ASN
+GLY
+SER
+THR
+LYS
+TRP
+TYR
+GLN
+ASN
+GLY
+SER
+THR
+LYS
+ILE
+TYR
+THR
Added: SwiftApps/CMTS/stringmethod/src/RESIDUE_NAMES_2
===================================================================
--- SwiftApps/CMTS/stringmethod/src/RESIDUE_NAMES_2 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/RESIDUE_NAMES_2 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
+CA THR
+CB THR
+CA TRP
+CB TRP
+CA ILE
+CB ILE
+CA GLN
+CB GLN
+CA ASN
+CB ASN
+CA GLY
+CA SER
+CB SER
+CA THR
+CB THR
+CA LYS
+CB LYS
+CA TRP
+CB TRP
+CA TYR
+CB TYR
+CA GLN
+CB GLN
+CA ASN
+CB ASN
+CA GLY
+CA SER
+CB SER
+CA THR
+CB THR
+CA LYS
+CB LYS
+CA ILE
+CB ILE
+CA TYR
+CB TYR
+CA THR
+CB THR
Added: SwiftApps/CMTS/stringmethod/src/SIMULPARAMS_NAMD_UNIT
===================================================================
--- SwiftApps/CMTS/stringmethod/src/SIMULPARAMS_NAMD_UNIT (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/SIMULPARAMS_NAMD_UNIT 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,10 @@
+run_length_time_steps 10000
+timestep 1.0
+collision_frequency_timestep 1
+temperature 330.0
+config_save_frequency 50000
+progress_frequency 50000
+write_frequency_other 50000
+write_frequency_rmsd 1000
+write_frequency_pdb_traj 50000
+
Added: SwiftApps/CMTS/stringmethod/src/calc_rmsd_from_one_structure.c
===================================================================
--- SwiftApps/CMTS/stringmethod/src/calc_rmsd_from_one_structure.c (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/calc_rmsd_from_one_structure.c 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,50 @@
+/* Calculate rmsd of the current configuration from a fixed state*/
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <time.h>
+#include <string.h>
+
+#include "calc_rmsd_from_one_structure.h"
+
+double Calc_rmsd(FR_DAT *fr, FR_DAT *fr_fixed_state)
+{
+ double msd, rmsd, dis1, dis2, dif, DEL_X, DEL_Y, DEL_Z;
+ int i,j;
+ msd = 0.0;
+// for(i = 0 ; i < fr->natoms; i++)
+ for(i = 0 ; i < fr->natoms-1; i++)
+ {
+ for(j=i+1; j<fr->natoms; j++){
+ DEL_X = (fr->x[i][0]-fr->x[j][0]);
+ DEL_Y = (fr->x[i][1]-fr->x[j][1]);
+ DEL_Z = (fr->x[i][2]-fr->x[j][2]);
+ dis1 = pow(DEL_X,2)+pow(DEL_Y,2)+pow(DEL_Z,2);
+ dis1 = sqrt(dis1);
+
+ DEL_X = (fr_fixed_state->x[i][0]-fr_fixed_state->x[j][0]);
+ DEL_Y = (fr_fixed_state->x[i][1]-fr_fixed_state->x[j][1]);
+ DEL_Z = (fr_fixed_state->x[i][2]-fr_fixed_state->x[j][2]);
+ dis2 = pow(DEL_X,2)+pow(DEL_Y,2)+pow(DEL_Z,2);
+ dis2 = sqrt(dis2);
+
+ dif = dis1-dis2;
+
+ msd += pow(dif,2);
+
+ }
+
+// DEL_X = fr->x[i][0] - fr_fixed_state->x[i][0];
+ // DEL_Y = fr->x[i][1] - fr_fixed_state->x[i][1];
+ // DEL_Z = fr->x[i][2] - fr_fixed_state->x[i][2];
+ // msd = msd + pow(DEL_X, 2) + pow(DEL_Y, 2) + pow(DEL_Z, 2);
+ }
+// msd = msd / ((double)fr->natoms);
+ msd = msd / (fr->natoms * (fr->natoms-1)*0.5);
+ rmsd = sqrt(msd);
+ return rmsd;
+}
+
+
Added: SwiftApps/CMTS/stringmethod/src/calc_rmsd_from_one_structure.h
===================================================================
--- SwiftApps/CMTS/stringmethod/src/calc_rmsd_from_one_structure.h (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/calc_rmsd_from_one_structure.h 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,8 @@
+#ifndef _calc_rmsd_from_one_structure_h
+#define _calc_rmsd_from_one_structure_h
+
+#include "md_ld_common_d_dimension_namd.h"
+
+double Calc_rmsd(FR_DAT *fr, FR_DAT *fr_fixed_state);
+
+#endif
Added: SwiftApps/CMTS/stringmethod/src/common_functions.c
===================================================================
--- SwiftApps/CMTS/stringmethod/src/common_functions.c (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/common_functions.c 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,351 @@
+/* Last modified on Septemeber 29, 2011. */
+
+/* Modifications are made to make the functions work for
+ * a d-dimensional system.
+ * */
+
+/* Data type 'matrix' is remaned to 'my_matrix' to avoid conflict with
+ * Numerical Recipes data type with the same name.*/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <string.h>
+#include <time.h>
+#include <sys/time.h>
+
+#include "common_functions.h"
+
+/*each component of a position vector is within [0.0, box_length]
+ index_for_coponent = 0 for x
+ index_for_coponent = 1 for y
+ index_for_coponent = 2 for z
+*/
+double celladjustOneComp(double OneCompOfVector, int index_of_component, my_matrix box)
+{
+ double BoxLength;
+ double CorrectedComponent;
+ CorrectedComponent = OneCompOfVector;
+ BoxLength = box[index_of_component][index_of_component];
+ if((CorrectedComponent > BoxLength) || (CorrectedComponent < 0))
+ {
+ if(CorrectedComponent > BoxLength)
+ {
+ while(CorrectedComponent > BoxLength)
+ {
+ CorrectedComponent = CorrectedComponent - BoxLength;
+ }
+ }
+ else
+ {
+ while(CorrectedComponent < 0)
+ {
+ CorrectedComponent = CorrectedComponent + BoxLength;
+ }
+ }
+ }
+
+ return CorrectedComponent;
+}
+
+/* adjusts the position vector of all the particles to keep them inside the
+ central box for one frame (or config)*/
+void celladjust_one_config(FR_DAT *const fr)
+{
+ int dim = DIMENSION;
+ int d;
+ int NumParticles = fr->natoms;
+ double current_value;
+ /*
+ double xComponent;
+ double yComponent;
+ double zComponent;
+ */
+
+ int j;
+
+ for (j = 0 ; j < NumParticles ; j++)
+ {
+ /*
+ xComponent = fr->x[j][0];
+ yComponent = fr->x[j][1];
+ zComponent = fr->x[j][2];
+
+ fr->x[j][0] = celladjustOneComp(xComponent, 0, fr->box);
+ fr->x[j][1] = celladjustOneComp(yComponent, 1, fr->box);
+ fr->x[j][2] = celladjustOneComp(zComponent, 2, fr->box);
+ */
+
+ for(d = 0 ; d < dim ; d++)
+ {
+ current_value = fr->x[j][d];
+ fr->x[j][d] = celladjustOneComp(current_value, d, fr->box);
+ }
+ }
+}
+
+
+/*each component of a position vector is within [-box_length/2, box_length/2]
+ index_for_coponent = 0 for x
+ index_for_coponent = 1 for y
+ index_for_coponent = 2 for z
+*/
+double celladjustOneComp_origin_box_center(double OneCompOfVector, int index_of_component, my_matrix box)
+{
+ double BoxLength, Half_BoxLength;
+ double CorrectedComponent;
+ CorrectedComponent = OneCompOfVector;
+ BoxLength = box[index_of_component][index_of_component];
+ Half_BoxLength = box[index_of_component][index_of_component] / 2;
+ if((CorrectedComponent > Half_BoxLength) || (CorrectedComponent < (-Half_BoxLength)))
+ {
+ if(CorrectedComponent > Half_BoxLength)
+ {
+ while(CorrectedComponent > Half_BoxLength)
+ {
+ CorrectedComponent = CorrectedComponent - BoxLength;
+ }
+ }
+ if(CorrectedComponent < (-Half_BoxLength))
+ {
+ while(CorrectedComponent < (-Half_BoxLength))
+ {
+ CorrectedComponent = CorrectedComponent + BoxLength;
+ }
+ }
+ }
+
+ return CorrectedComponent;
+}
+
+
+
+/* adjusts the position vector of all the particles to keep them inside the
+ central box for one frame (or config)*/
+void celladjust_one_config_origin_box_center(FR_DAT *const fr)
+{
+ int dim = DIMENSION;
+ int d;
+ int NumParticles = fr->natoms;
+ double current_value;
+ /*
+ double xComponent;
+ double yComponent;
+ double zComponent;
+ */
+
+ int j;
+
+ for (j = 0 ; j < NumParticles ; j++)
+ {
+ /*
+ xComponent = fr->x[j][0];
+ yComponent = fr->x[j][1];
+ zComponent = fr->x[j][2];
+
+ fr->x[j][0] = celladjustOneComp(xComponent, 0, fr->box);
+ fr->x[j][1] = celladjustOneComp(yComponent, 1, fr->box);
+ fr->x[j][2] = celladjustOneComp(zComponent, 2, fr->box);
+ */
+
+ for(d = 0 ; d < dim ; d++)
+ {
+ current_value = fr->x[j][d];
+ fr->x[j][d] = celladjustOneComp_origin_box_center(current_value, d, fr->box);
+ }
+ }
+}
+
+
+
+
+/*Corrects the drift of the system. Total momentun of the system should be zero*/
+int velocenter(FR_DAT *const fr)
+{
+ int i,d;
+ int dim;
+ double totmass;
+ /*
+ double netvelx, netvely, netvelz;
+ double driftx, drifty, driftz;
+ driftx = 0;
+ drifty = 0;
+ driftz = 0;
+ */
+ double drift[DIMENSION], net_velocity_correction[DIMENSION];
+
+ dim = DIMENSION;
+ totmass = 0;
+ for(d = 0 ; d < dim ; d++)
+ {
+ drift[d] = 0;
+ }
+
+ /* calculate the mean "drift" of the system and correct */
+ for (i = 0; i < fr->natoms; i++)
+ {
+ /*
+ driftx = driftx + (fr->v[i][0] * fr->m[i]);
+ drifty = drifty + (fr->v[i][1] * fr->m[i]);
+ driftz = driftz + (fr->v[i][2] * fr->m[i]);
+ */
+ for(d = 0 ; d < dim ; d++)
+ {
+ drift[d] = drift[d] + (fr->v[i][d] * fr->m[i]);
+ }
+ totmass = totmass + fr->m[i]; /* Find the total mass of the system */
+ }
+ /*
+ netvelx = driftx / totmass;
+ netvely = drifty / totmass;
+ netvelz = driftz / totmass;
+ */
+ /* Find the amount by which to correct the velocities.*/
+ for(d = 0 ; d < dim ; d++)
+ {
+ net_velocity_correction[d] = drift[d] / totmass;
+ }
+ /* Correct velocities */
+ for (i = 0; i < fr->natoms; i++)
+ {
+ /*
+ fr->v[i][0] = fr->v[i][0] - netvelx;
+ fr->v[i][1] = fr->v[i][1] - netvely;
+ fr->v[i][2] = fr->v[i][2] - netvelz;
+ */
+ for(d = 0 ; d < dim ; d++)
+ {
+ fr->v[i][d] = fr->v[i][d] - net_velocity_correction[d];
+ }
+ }
+ return 0;
+}
+
+
+
+/*Generates random numbers from standard normal distributions*/
+double getnorm()
+{
+ double normx, normy, w;
+ w = 1.1;
+ while (w > 1.0)
+ {
+ normx = (double) rand() / ((double) RAND_MAX + 1);
+ normy = (double) rand() / ((double) RAND_MAX + 1);
+ normx = (2.0 * normx) - 1.0;
+ normy = (2.0 * normy) - 1.0;
+ w = (normx * normx) + (normy * normy);
+ }
+ w = (-2.0 * log(w)) / w;
+ w = sqrt(w);
+ return (normx * w);
+}
+
+void seed_rand(int thread_n, struct drand48_data *buffer)
+{
+ struct timeval tv;
+
+ gettimeofday(&tv, NULL);
+ srand48_r(tv.tv_sec*thread_n + tv.tv_usec, buffer);
+}
+
+
+double getnorm_omp(struct drand48_data *drand_buffer)
+{
+ double normx, normy, w;
+ w = 1.1;
+ while (w > 1.0)
+ {
+ drand48_r(drand_buffer, &normx);
+ drand48_r(drand_buffer, &normy);
+ normx = (2.0 * normx) - 1.0;
+ normy = (2.0 * normy) - 1.0;
+ w = (normx * normx) + (normy * normy);
+ }
+ w = (-2.0 * log(w)) / w;
+ w = sqrt(w);
+ return (normx * w);
+}
+
+
+/*randomizes the velocity of each particle.
+ The Maxwell-Boltzmann distribution is exp(-mv^2 / 2k_bT). Where m is mass
+ and k_b is the Boltzmann constant. In LJ reduced unit the Boltzmann constant
+ is 1. BUT IN ANY OTHER UNIT IT IS NOT 1.
+
+ BOLTZMANN CONSTANT IS #defined IN THE FILE 'md_common_structures.h'
+*/
+void getvelocities(FR_DAT *const fr, double temperature)
+{
+ int i, d;
+ int dim = DIMENSION;
+ double normfoo;
+ double factor, factor_temp;
+ double k_b = BOLTZMANN_CONSTANT; /*This is the Boltzmann constant */
+ double k_bT = k_b * temperature;
+ for (i = 0; i < fr->natoms; i++)
+ {
+ factor_temp = k_bT / fr->m[i];
+ factor = sqrt(factor_temp);
+
+ /*
+ normfoo = getnorm();
+ fr->v[i][0] = normfoo * factor;
+ normfoo = getnorm();
+ fr->v[i][1] = normfoo * factor;
+ normfoo = getnorm();
+ fr->v[i][2] = normfoo * factor;
+ */
+
+ for(d = 0 ; d < dim ; d++)
+ {
+ normfoo = getnorm();
+ fr->v[i][d] = normfoo * factor;
+ }
+ }
+}
+
+
+
+/*Randomize the random number generator*/
+void Randomize(void)
+{
+ srand((int) time(NULL));
+}
+
+
+
+/* Calculates kinetic energy of the system*/
+void get_kinetic_energy(FR_DAT *const fr)
+{
+ int i, j;
+ int dim = DIMENSION;
+ double total_KE, velocity_squared;
+
+ total_KE = 0.0;
+
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ velocity_squared = 0.0;
+ for(j = 0 ; j < dim ; j++)
+ {
+ velocity_squared = velocity_squared + (fr->v[i][j] * fr->v[i][j]);
+ }
+ total_KE = total_KE + ((fr->m[i] * velocity_squared) / 2);
+ }
+
+ fr->K = total_KE;
+}
+
+
+
+/*allocate configuration data structure. Num_atoms is the total number of atoms in the
+ topology file.*/
+void Alloc_main_data_structure(int Num_atoms, FR_DAT *const fr)
+{
+ fr->natoms = Num_atoms;
+ fr->x = (rvec *)malloc(Num_atoms * sizeof(rvec));
+ fr->f = (rvec *)malloc(Num_atoms * sizeof(rvec));
+ fr->v = (rvec *)malloc(Num_atoms * sizeof(rvec));
+ fr->m = (double *)malloc(Num_atoms * sizeof(double));
+}
Added: SwiftApps/CMTS/stringmethod/src/common_functions.h
===================================================================
--- SwiftApps/CMTS/stringmethod/src/common_functions.h (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/common_functions.h 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,29 @@
+#ifndef _commmon_functions_h
+#define _commmon_functions_h
+
+#include "md_ld_common_d_dimension_namd.h"
+
+
+double celladjustOneComp(double OneCompOfVector, int index_of_component, my_matrix box);
+
+void celladjust_one_config(FR_DAT *const fr);
+
+double celladjustOneComp_origin_box_center(double OneCompOfVector, int index_of_component, my_matrix box);
+
+void celladjust_one_config_origin_box_center(FR_DAT *const fr);
+
+int velocenter(FR_DAT *const fr);
+
+double getnorm();
+double getnorm_omp(struct drand48_data *buffer);
+void seed_rand(int thread_n, struct drand48_data *buffer);
+
+void getvelocities(FR_DAT *const fr, double temperature);
+
+void Randomize(void);
+
+void get_kinetic_energy(FR_DAT *const fr);
+
+void Alloc_main_data_structure(int Num_atoms, FR_DAT *const fr);
+
+#endif
Added: SwiftApps/CMTS/stringmethod/src/data/CONSTRAINS-EXT-EXT
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/CONSTRAINS-EXT-EXT (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/CONSTRAINS-EXT-EXT 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,190 @@
+1 2
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Added: SwiftApps/CMTS/stringmethod/src/data/CONSTRAINS-EXT-EXT_2
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/CONSTRAINS-EXT-EXT_2 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/CONSTRAINS-EXT-EXT_2 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,190 @@
+1 3
+1 5
+1 7
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Added: SwiftApps/CMTS/stringmethod/src/data/CONSTRAINS-EXT-EXT_2b
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/CONSTRAINS-EXT-EXT_2b (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/CONSTRAINS-EXT-EXT_2b 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,513 @@
+1 2
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Added: SwiftApps/CMTS/stringmethod/src/data/CONSTRAINS-FINE
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/CONSTRAINS-FINE (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/CONSTRAINS-FINE 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,18 @@
+1 2
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Added: SwiftApps/CMTS/stringmethod/src/data/Collective_variables
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/Collective_variables (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/Collective_variables 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,32 @@
+0 0 3.831527 3.782441 6.107011 6.900732 13.109579 15.287681 9.874438 5.000012 7.699298 8.661628
+0 1 3.779334 3.860894 5.940840 6.174461 13.048871 15.214584 9.148716 8.438458 9.007326 9.213400
+0 2 3.830737 3.800230 6.534427 6.686247 11.424697 19.937717 10.243602 9.843754 4.866159 6.713856
+0 3 3.849425 3.842446 6.722404 5.880618 13.374562 20.817290 10.797561 8.419994 4.663196 6.093820
+0 4 3.793028 3.717703 6.784164 5.937693 11.897993 18.792287 10.115128 10.115484 5.141281 7.237922
+0 5 3.866983 3.574116 6.334034 5.819766 11.393858 19.152128 10.483889 9.783663 5.110163 6.361870
+0 6 3.853641 3.786616 6.818608 5.622758 12.342104 16.406889 10.106986 12.358208 13.032486 8.909891
+0 7 3.766150 3.735685 6.473705 5.357016 11.982710 13.254981 10.186293 12.304869 13.862113 9.195431
+0 8 3.785387 3.827355 5.995816 5.401364 9.864877 13.249189 9.816330 10.453122 9.260142 9.137624
+0 9 3.843174 3.744445 5.726239 5.638223 10.720817 14.393929 9.828190 10.909055 9.416503 8.666825
+0 10 3.734337 3.565081 5.970250 6.975698 12.372368 16.038509 9.217428 6.686031 4.938071 7.401203
+0 11 3.833039 3.778662 6.543028 6.950622 13.179322 17.551584 9.187647 7.897839 5.925705 7.777599
+0 12 3.929236 3.860027 6.421612 6.816851 13.404619 18.381737 10.060073 8.125581 5.141397 7.733524
+0 13 3.848630 3.942751 6.737077 6.018969 12.256424 15.473095 9.683735 8.840863 6.400442 7.641747
+0 14 3.838187 3.822196 6.723312 7.398608 13.235729 17.329774 9.918712 8.365379 4.766475 8.065716
+0 15 3.781928 3.719291 6.971546 5.556624 13.256601 16.638606 10.265926 9.072560 5.064256 8.652168
+0 16 3.869139 3.772115 6.277554 5.412293 12.934618 16.015789 9.917453 6.713257 6.050427 7.962784
+0 17 3.682434 3.801485 6.159870 7.270758 12.432839 15.550430 10.197148 7.293642 6.008312 7.704114
+0 18 3.875891 3.828869 6.436879 6.168097 13.079115 16.785724 10.490460 7.107639 6.455567 8.013552
+0 19 3.852016 3.778416 6.580046 6.350045 13.148167 16.828407 9.833160 6.937880 6.373135 7.594816
+0 20 3.750237 3.817316 6.279734 6.534893 13.561698 16.437433 10.207687 5.878450 6.158243 7.856034
+0 21 3.756657 3.908393 6.463885 6.953997 12.669701 15.746152 9.810652 6.591883 6.242859 8.352322
+0 22 3.815720 3.738434 6.293754 6.928745 13.408405 16.761640 9.999777 6.456647 6.078242 8.063598
+0 23 3.813483 3.827916 6.273652 6.355417 12.735507 15.953733 9.704330 5.970057 6.484220 8.319103
+0 24 3.742577 3.859782 5.939889 6.335079 11.864200 15.839733 10.125602 5.835627 6.344457 8.198559
+0 25 3.822746 3.771793 6.068379 6.709940 10.894249 14.593422 9.286351 5.729348 6.261783 7.672749
+0 26 3.884303 3.850217 5.776226 6.227587 12.020084 15.054181 9.882700 5.896289 6.164118 7.448675
+0 27 3.918662 3.752612 6.066897 5.227248 11.839707 15.122735 9.600372 7.131305 6.553195 8.158695
+0 28 3.791573 3.678478 6.263798 5.908245 13.119965 15.278878 9.577989 5.480450 6.540680 7.871971
+0 29 3.760805 3.869954 6.056218 5.677654 10.949509 14.305595 9.284054 10.173751 8.364085 8.323965
+0 30 3.746624 3.803044 6.448435 5.512967 10.617817 12.149812 9.816585 7.711455 6.274965 7.807024
+0 31 3.808333 3.868616 6.159983 6.679146 12.027385 15.535831 9.996235 6.387393 6.743463 7.867280
Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_0
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_0 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_0 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+24.673 12.849 -5.563
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_1
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_1 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_1 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+23.546 11.933 -4.152
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_10
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_10 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_10 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+24.419 12.685 -3.263
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_11
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_11 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_11 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+23.950 12.754 -2.687
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_12
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_12 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_12 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+23.915 12.437 -2.833
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_13
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_13 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_13 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+23.321 12.731 -3.752
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_14
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_14 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_14 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+24.422 13.210 -4.270
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_15
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_15 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_15 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+24.249 12.885 -3.482
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_16
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_16 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_16 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_17
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_17 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_17 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_18
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_18 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_18 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_19
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_19 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_19 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
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+27.090 23.804 -1.765
Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
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+31.204 17.202 1.406
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_20
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_20 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_20 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_21
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_21 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_21 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_22
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_22 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_22 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
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+29.792 22.514 0.032
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_23
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_23 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_23 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
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+34.453 13.855 -0.363
+31.540 15.997 1.100
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+27.063 24.177 -1.291
Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_24
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_24 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_24 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
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+31.924 16.390 1.089
+31.183 19.462 -1.038
+29.391 22.295 0.744
+27.224 23.985 -1.885
Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_25
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_25 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_25 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
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+30.862 16.111 0.682
+31.403 19.264 -1.301
+29.573 22.401 0.176
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_26
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_26 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_26 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_27
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_27 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_27 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_28
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_28 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_28 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_29
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_29 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_29 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_0
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_0 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_0 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_1
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_1 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_1 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_10
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_10 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_10 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_11
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_11 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_11 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_12
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_12 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_12 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_13
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_13 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_13 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_14
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_14 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_14 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_15
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_15 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_15 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_16
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_16 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_16 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_17
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_17 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_17 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_18
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_18 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_18 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_19
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_19 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_19 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_2
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_2 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_2 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_20
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_20 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_20 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_21
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_21 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_21 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_22
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_22 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_22 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_23
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_23 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_23 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_24
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_24 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_24 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_25
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_25 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_25 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_26
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_26 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_26 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_27
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_27 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_27 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_28
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_28 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_28 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_29
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_29 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_29 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_3
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_3 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_3 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_30
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_30 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_30 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_31
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_31 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_31 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_4
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_4 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_4 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_5
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_5 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_5 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_6
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_6 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_6 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_7
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_7 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_7 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_8
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_8 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_8 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_9
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_9 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_2_9 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_3
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_3 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_3 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_30
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_30 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_30 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_31
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_31 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_31 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_4
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_4 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_4 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+25.693 13.770 -4.875
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_5
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_5 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_5 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_6
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_6 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_6 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_7
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_7 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_7 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
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+30.595 20.819 10.004
Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_8
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_8 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_8 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
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Added: SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_9
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_9 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/INITIAL_CONFIG_C_ALPHA_9 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+24.035 13.320 -4.882
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+18.274 23.699 4.669
+21.392 23.683 2.420
+21.388 21.988 -0.938
+24.885 20.857 -1.728
+26.404 18.311 -4.108
+28.370 15.289 -2.981
+30.730 13.627 -5.396
+29.909 10.201 -4.129
+31.606 9.694 -0.709
+33.427 12.862 0.165
+31.911 15.641 2.314
+34.066 18.760 2.418
+31.425 21.293 3.279
+30.831 20.349 7.034
Added: SwiftApps/CMTS/stringmethod/src/data/elastic-network-potential-energy
===================================================================
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_0.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_0.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_0.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.673 12.849 -5.563 1.00 1.00 A C
+ATOM 2 CA TRP A 2 23.214 16.010 -3.963 1.00 1.00 A C
+ATOM 3 CA ILE A 3 21.548 16.254 -0.576 1.00 1.00 A C
+ATOM 4 CA GLN A 4 20.016 19.808 -0.155 1.00 1.00 A C
+ATOM 5 CA ASN A 5 19.099 20.043 3.540 1.00 1.00 A C
+ATOM 6 CA GLY A 6 18.524 23.803 3.815 1.00 1.00 A C
+ATOM 7 CA SER A 7 21.444 25.372 5.538 1.00 1.00 A C
+ATOM 8 CA THR A 8 24.070 22.640 4.658 1.00 1.00 A C
+ATOM 9 CA LYS A 9 24.134 20.811 1.513 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.793 17.385 1.534 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.436 15.607 -1.401 1.00 1.00 A C
+ATOM 12 CA GLN A 12 27.949 11.896 -1.672 1.00 1.00 A C
+ATOM 13 CA ASN A 13 30.575 11.904 -4.260 1.00 1.00 A C
+ATOM 14 CA GLY A 14 32.990 9.317 -2.740 1.00 1.00 A C
+ATOM 15 CA SER A 15 34.181 10.934 0.395 1.00 1.00 A C
+ATOM 16 CA THR A 16 31.643 13.473 1.511 1.00 1.00 A C
+ATOM 17 CA LYS A 17 31.955 17.104 0.909 1.00 1.00 A C
+ATOM 18 CA ILE A 18 30.593 20.181 2.548 1.00 1.00 A C
+ATOM 19 CA TYR A 19 28.636 22.877 0.832 1.00 1.00 A C
+ATOM 20 CA THR A 20 26.003 25.623 1.670 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_1.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_1.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_1.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 23.546 11.933 -4.152 1.00 1.00 A C
+ATOM 2 CA TRP A 2 23.092 15.533 -3.095 1.00 1.00 A C
+ATOM 3 CA ILE A 3 21.586 16.045 0.423 1.00 1.00 A C
+ATOM 4 CA GLN A 4 19.383 19.118 -0.271 1.00 1.00 A C
+ATOM 5 CA ASN A 5 18.924 20.615 3.129 1.00 1.00 A C
+ATOM 6 CA GLY A 6 17.682 24.082 2.309 1.00 1.00 A C
+ATOM 7 CA SER A 7 20.285 25.605 0.166 1.00 1.00 A C
+ATOM 8 CA THR A 8 23.149 23.575 1.748 1.00 1.00 A C
+ATOM 9 CA LYS A 9 23.540 20.884 -0.781 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.473 18.167 1.163 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.403 16.255 -1.719 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.017 12.473 -1.486 1.00 1.00 A C
+ATOM 13 CA ASN A 13 29.157 11.132 -4.922 1.00 1.00 A C
+ATOM 14 CA GLY A 14 33.003 11.091 -5.274 1.00 1.00 A C
+ATOM 15 CA SER A 15 33.863 13.286 -2.370 1.00 1.00 A C
+ATOM 16 CA THR A 16 31.872 13.825 0.775 1.00 1.00 A C
+ATOM 17 CA LYS A 17 31.403 17.638 1.008 1.00 1.00 A C
+ATOM 18 CA ILE A 18 30.057 18.320 4.446 1.00 1.00 A C
+ATOM 19 CA TYR A 19 29.835 22.075 4.711 1.00 1.00 A C
+ATOM 20 CA THR A 20 30.651 23.250 8.229 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_10.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_10.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_10.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.419 12.685 -3.263 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.276 15.712 -2.827 1.00 1.00 A C
+ATOM 3 CA ILE A 3 21.226 16.432 0.503 1.00 1.00 A C
+ATOM 4 CA GLN A 4 18.950 19.482 1.186 1.00 1.00 A C
+ATOM 5 CA ASN A 5 19.978 20.507 4.684 1.00 1.00 A C
+ATOM 6 CA GLY A 6 17.949 23.676 4.912 1.00 1.00 A C
+ATOM 7 CA SER A 7 20.481 26.308 3.873 1.00 1.00 A C
+ATOM 8 CA THR A 8 23.516 24.060 3.804 1.00 1.00 A C
+ATOM 9 CA LYS A 9 23.314 22.350 0.393 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.297 19.185 1.008 1.00 1.00 A C
+ATOM 11 CA TYR A 11 26.810 17.848 -2.156 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.656 14.531 -1.801 1.00 1.00 A C
+ATOM 13 CA ASN A 13 30.468 12.966 -4.798 1.00 1.00 A C
+ATOM 14 CA GLY A 14 29.975 9.649 -3.202 1.00 1.00 A C
+ATOM 15 CA SER A 15 32.431 9.524 -0.294 1.00 1.00 A C
+ATOM 16 CA THR A 16 33.863 12.946 0.247 1.00 1.00 A C
+ATOM 17 CA LYS A 17 31.233 15.535 1.105 1.00 1.00 A C
+ATOM 18 CA ILE A 18 32.610 18.526 -0.756 1.00 1.00 A C
+ATOM 19 CA TYR A 19 29.870 21.300 -0.394 1.00 1.00 A C
+ATOM 20 CA THR A 20 29.756 21.993 3.370 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_11.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_11.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_11.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 23.950 12.754 -2.687 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.225 16.096 -1.947 1.00 1.00 A C
+ATOM 3 CA ILE A 3 21.865 16.333 1.807 1.00 1.00 A C
+ATOM 4 CA GLN A 4 19.133 18.680 2.451 1.00 1.00 A C
+ATOM 5 CA ASN A 5 19.492 21.524 5.006 1.00 1.00 A C
+ATOM 6 CA GLY A 6 17.493 24.579 3.882 1.00 1.00 A C
+ATOM 7 CA SER A 7 19.961 26.565 1.758 1.00 1.00 A C
+ATOM 8 CA THR A 8 23.048 24.417 2.185 1.00 1.00 A C
+ATOM 9 CA LYS A 9 22.580 21.150 0.360 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.653 19.062 0.978 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.037 17.293 -2.028 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.326 13.916 -1.140 1.00 1.00 A C
+ATOM 13 CA ASN A 13 29.714 13.147 -4.590 1.00 1.00 A C
+ATOM 14 CA GLY A 14 30.463 9.490 -4.662 1.00 1.00 A C
+ATOM 15 CA SER A 15 33.694 9.112 -2.701 1.00 1.00 A C
+ATOM 16 CA THR A 16 34.195 12.758 -1.628 1.00 1.00 A C
+ATOM 17 CA LYS A 17 32.016 15.521 -0.003 1.00 1.00 A C
+ATOM 18 CA ILE A 18 32.618 19.021 -1.280 1.00 1.00 A C
+ATOM 19 CA TYR A 19 30.441 20.995 1.106 1.00 1.00 A C
+ATOM 20 CA THR A 20 30.925 19.995 4.714 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_12.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_12.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_12.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 23.915 12.437 -2.833 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.386 15.820 -1.546 1.00 1.00 A C
+ATOM 3 CA ILE A 3 22.086 16.261 2.277 1.00 1.00 A C
+ATOM 4 CA GLN A 4 19.380 18.674 3.159 1.00 1.00 A C
+ATOM 5 CA ASN A 5 19.855 20.660 6.389 1.00 1.00 A C
+ATOM 6 CA GLY A 6 18.264 23.986 7.049 1.00 1.00 A C
+ATOM 7 CA SER A 7 18.738 25.910 3.879 1.00 1.00 A C
+ATOM 8 CA THR A 8 21.878 24.973 2.416 1.00 1.00 A C
+ATOM 9 CA LYS A 9 22.116 21.370 0.839 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.483 19.651 0.700 1.00 1.00 A C
+ATOM 11 CA TYR A 11 26.630 17.372 -2.150 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.696 14.386 -1.495 1.00 1.00 A C
+ATOM 13 CA ASN A 13 29.715 12.409 -4.568 1.00 1.00 A C
+ATOM 14 CA GLY A 14 30.319 8.879 -3.239 1.00 1.00 A C
+ATOM 15 CA SER A 15 33.683 9.250 -1.576 1.00 1.00 A C
+ATOM 16 CA THR A 16 34.923 12.834 -1.655 1.00 1.00 A C
+ATOM 17 CA LYS A 17 32.838 15.615 -0.395 1.00 1.00 A C
+ATOM 18 CA ILE A 18 32.778 18.832 -2.439 1.00 1.00 A C
+ATOM 19 CA TYR A 19 30.068 20.939 -0.775 1.00 1.00 A C
+ATOM 20 CA THR A 20 31.498 21.332 2.723 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_13.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_13.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_13.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 23.321 12.731 -3.752 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.189 16.128 -2.341 1.00 1.00 A C
+ATOM 3 CA ILE A 3 21.974 15.695 1.572 1.00 1.00 A C
+ATOM 4 CA GLN A 4 20.358 18.509 3.401 1.00 1.00 A C
+ATOM 5 CA ASN A 5 21.674 20.134 6.631 1.00 1.00 A C
+ATOM 6 CA GLY A 6 18.559 22.348 6.596 1.00 1.00 A C
+ATOM 7 CA SER A 7 18.723 24.887 3.895 1.00 1.00 A C
+ATOM 8 CA THR A 8 22.402 24.166 3.181 1.00 1.00 A C
+ATOM 9 CA LYS A 9 22.194 21.105 1.138 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.684 19.589 0.431 1.00 1.00 A C
+ATOM 11 CA TYR A 11 26.352 17.430 -2.546 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.101 14.177 -1.938 1.00 1.00 A C
+ATOM 13 CA ASN A 13 30.394 13.185 -4.838 1.00 1.00 A C
+ATOM 14 CA GLY A 14 30.278 9.509 -3.970 1.00 1.00 A C
+ATOM 15 CA SER A 15 32.400 9.405 -0.743 1.00 1.00 A C
+ATOM 16 CA THR A 16 33.550 12.957 0.242 1.00 1.00 A C
+ATOM 17 CA LYS A 17 31.086 15.777 0.326 1.00 1.00 A C
+ATOM 18 CA ILE A 18 32.309 18.411 -1.981 1.00 1.00 A C
+ATOM 19 CA TYR A 19 30.841 21.576 -0.642 1.00 1.00 A C
+ATOM 20 CA THR A 20 32.252 23.275 2.592 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_14.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_14.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_14.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.422 13.210 -4.270 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.624 15.829 -2.116 1.00 1.00 A C
+ATOM 3 CA ILE A 3 23.196 15.863 1.663 1.00 1.00 A C
+ATOM 4 CA GLN A 4 20.058 17.420 3.035 1.00 1.00 A C
+ATOM 5 CA ASN A 5 19.770 19.885 5.821 1.00 1.00 A C
+ATOM 6 CA GLY A 6 16.963 22.270 4.795 1.00 1.00 A C
+ATOM 7 CA SER A 7 19.386 25.207 5.037 1.00 1.00 A C
+ATOM 8 CA THR A 8 22.947 24.142 4.134 1.00 1.00 A C
+ATOM 9 CA LYS A 9 22.673 21.495 1.497 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.962 19.675 0.755 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.125 17.980 -2.420 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.785 14.662 -2.342 1.00 1.00 A C
+ATOM 13 CA ASN A 13 30.874 12.584 -4.720 1.00 1.00 A C
+ATOM 14 CA GLY A 14 29.992 9.290 -3.004 1.00 1.00 A C
+ATOM 15 CA SER A 15 31.881 10.055 0.268 1.00 1.00 A C
+ATOM 16 CA THR A 16 34.162 13.086 -0.326 1.00 1.00 A C
+ATOM 17 CA LYS A 17 32.466 16.502 -0.373 1.00 1.00 A C
+ATOM 18 CA ILE A 18 32.805 19.002 -3.256 1.00 1.00 A C
+ATOM 19 CA TYR A 19 30.292 21.512 -1.957 1.00 1.00 A C
+ATOM 20 CA THR A 20 30.535 22.144 1.734 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_15.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_15.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_15.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.249 12.885 -3.482 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.632 15.862 -1.801 1.00 1.00 A C
+ATOM 3 CA ILE A 3 23.160 15.596 1.871 1.00 1.00 A C
+ATOM 4 CA GLN A 4 20.481 17.553 3.855 1.00 1.00 A C
+ATOM 5 CA ASN A 5 20.622 18.794 7.522 1.00 1.00 A C
+ATOM 6 CA GLY A 6 17.047 20.185 7.631 1.00 1.00 A C
+ATOM 7 CA SER A 7 17.652 23.644 6.004 1.00 1.00 A C
+ATOM 8 CA THR A 8 21.142 22.976 4.870 1.00 1.00 A C
+ATOM 9 CA LYS A 9 22.224 21.392 1.674 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.807 19.948 1.006 1.00 1.00 A C
+ATOM 11 CA TYR A 11 26.890 18.154 -2.137 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.612 14.763 -2.258 1.00 1.00 A C
+ATOM 13 CA ASN A 13 30.363 13.522 -5.358 1.00 1.00 A C
+ATOM 14 CA GLY A 14 30.821 9.837 -4.897 1.00 1.00 A C
+ATOM 15 CA SER A 15 32.075 9.710 -1.313 1.00 1.00 A C
+ATOM 16 CA THR A 16 33.161 13.055 0.193 1.00 1.00 A C
+ATOM 17 CA LYS A 17 31.680 16.401 0.674 1.00 1.00 A C
+ATOM 18 CA ILE A 18 32.952 19.269 -1.331 1.00 1.00 A C
+ATOM 19 CA TYR A 19 30.315 21.875 -2.402 1.00 1.00 A C
+ATOM 20 CA THR A 20 28.564 24.563 -0.415 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_16.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_16.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_16.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 23.974 12.646 -3.769 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.405 15.755 -2.083 1.00 1.00 A C
+ATOM 3 CA ILE A 3 22.693 15.783 1.678 1.00 1.00 A C
+ATOM 4 CA GLN A 4 20.617 18.789 2.532 1.00 1.00 A C
+ATOM 5 CA ASN A 5 20.339 19.250 6.352 1.00 1.00 A C
+ATOM 6 CA GLY A 6 18.218 21.978 7.807 1.00 1.00 A C
+ATOM 7 CA SER A 7 19.448 24.513 5.234 1.00 1.00 A C
+ATOM 8 CA THR A 8 22.971 23.244 4.508 1.00 1.00 A C
+ATOM 9 CA LYS A 9 23.438 21.510 1.236 1.00 1.00 A C
+ATOM 10 CA TRP A 10 26.523 19.434 0.960 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.193 17.309 -2.223 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.595 13.899 -2.045 1.00 1.00 A C
+ATOM 13 CA ASN A 13 30.657 13.367 -5.167 1.00 1.00 A C
+ATOM 14 CA GLY A 14 31.134 9.682 -4.332 1.00 1.00 A C
+ATOM 15 CA SER A 15 32.411 9.712 -0.758 1.00 1.00 A C
+ATOM 16 CA THR A 16 33.605 13.262 -0.309 1.00 1.00 A C
+ATOM 17 CA LYS A 17 31.182 15.927 0.608 1.00 1.00 A C
+ATOM 18 CA ILE A 18 31.794 19.283 -1.201 1.00 1.00 A C
+ATOM 19 CA TYR A 19 29.858 22.455 -0.484 1.00 1.00 A C
+ATOM 20 CA THR A 20 27.716 23.614 -3.365 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_17.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_17.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_17.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 23.994 12.669 -4.114 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.205 15.504 -2.590 1.00 1.00 A C
+ATOM 3 CA ILE A 3 22.559 15.626 1.193 1.00 1.00 A C
+ATOM 4 CA GLN A 4 19.754 18.051 1.930 1.00 1.00 A C
+ATOM 5 CA ASN A 5 19.998 19.217 5.493 1.00 1.00 A C
+ATOM 6 CA GLY A 6 17.487 21.861 5.194 1.00 1.00 A C
+ATOM 7 CA SER A 7 19.728 24.996 4.967 1.00 1.00 A C
+ATOM 8 CA THR A 8 23.338 23.453 5.222 1.00 1.00 A C
+ATOM 9 CA LYS A 9 23.152 21.149 2.408 1.00 1.00 A C
+ATOM 10 CA TRP A 10 26.287 19.339 0.930 1.00 1.00 A C
+ATOM 11 CA TYR A 11 26.894 17.702 -2.411 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.429 14.246 -2.174 1.00 1.00 A C
+ATOM 13 CA ASN A 13 31.096 13.695 -4.735 1.00 1.00 A C
+ATOM 14 CA GLY A 14 31.045 9.948 -4.411 1.00 1.00 A C
+ATOM 15 CA SER A 15 33.058 9.644 -1.217 1.00 1.00 A C
+ATOM 16 CA THR A 16 33.804 13.308 -0.388 1.00 1.00 A C
+ATOM 17 CA LYS A 17 31.001 15.374 1.058 1.00 1.00 A C
+ATOM 18 CA ILE A 18 31.678 18.928 0.193 1.00 1.00 A C
+ATOM 19 CA TYR A 19 29.936 22.295 -0.013 1.00 1.00 A C
+ATOM 20 CA THR A 20 29.753 23.181 -3.710 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_18.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_18.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_18.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.215 12.473 -4.133 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.396 15.422 -2.396 1.00 1.00 A C
+ATOM 3 CA ILE A 3 22.572 15.614 1.424 1.00 1.00 A C
+ATOM 4 CA GLN A 4 20.158 18.403 2.196 1.00 1.00 A C
+ATOM 5 CA ASN A 5 19.425 19.100 5.826 1.00 1.00 A C
+ATOM 6 CA GLY A 6 16.946 21.960 5.760 1.00 1.00 A C
+ATOM 7 CA SER A 7 19.332 25.036 5.613 1.00 1.00 A C
+ATOM 8 CA THR A 8 22.638 23.196 5.183 1.00 1.00 A C
+ATOM 9 CA LYS A 9 22.996 21.704 1.767 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.821 19.583 0.465 1.00 1.00 A C
+ATOM 11 CA TYR A 11 26.899 17.351 -2.415 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.541 14.014 -2.054 1.00 1.00 A C
+ATOM 13 CA ASN A 13 30.636 13.738 -5.155 1.00 1.00 A C
+ATOM 14 CA GLY A 14 31.084 10.047 -4.798 1.00 1.00 A C
+ATOM 15 CA SER A 15 33.402 9.701 -1.822 1.00 1.00 A C
+ATOM 16 CA THR A 16 34.217 13.328 -0.984 1.00 1.00 A C
+ATOM 17 CA LYS A 17 31.736 15.865 0.674 1.00 1.00 A C
+ATOM 18 CA ILE A 18 31.492 19.195 -1.052 1.00 1.00 A C
+ATOM 19 CA TYR A 19 29.853 22.519 0.083 1.00 1.00 A C
+ATOM 20 CA THR A 20 27.113 23.654 -2.460 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_19.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_19.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_19.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.425 12.824 -3.856 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.623 15.909 -2.416 1.00 1.00 A C
+ATOM 3 CA ILE A 3 22.456 15.514 1.338 1.00 1.00 A C
+ATOM 4 CA GLN A 4 19.671 17.868 2.550 1.00 1.00 A C
+ATOM 5 CA ASN A 5 19.525 19.046 6.053 1.00 1.00 A C
+ATOM 6 CA GLY A 6 17.165 21.897 6.317 1.00 1.00 A C
+ATOM 7 CA SER A 7 18.676 24.410 3.980 1.00 1.00 A C
+ATOM 8 CA THR A 8 22.359 23.490 3.771 1.00 1.00 A C
+ATOM 9 CA LYS A 9 22.869 20.925 1.087 1.00 1.00 A C
+ATOM 10 CA TRP A 10 26.241 19.231 0.929 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.373 17.821 -2.507 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.673 14.261 -2.089 1.00 1.00 A C
+ATOM 13 CA ASN A 13 30.929 12.848 -4.773 1.00 1.00 A C
+ATOM 14 CA GLY A 14 31.377 9.667 -2.959 1.00 1.00 A C
+ATOM 15 CA SER A 15 33.926 10.130 -0.373 1.00 1.00 A C
+ATOM 16 CA THR A 16 34.390 13.832 -0.730 1.00 1.00 A C
+ATOM 17 CA LYS A 17 31.886 16.587 0.129 1.00 1.00 A C
+ATOM 18 CA ILE A 18 31.398 20.060 -1.263 1.00 1.00 A C
+ATOM 19 CA TYR A 19 29.572 22.709 0.941 1.00 1.00 A C
+ATOM 20 CA THR A 20 27.090 23.804 -1.765 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.961 14.402 -5.078 1.00 1.00 A C
+ATOM 2 CA TRP A 2 23.326 17.516 -3.560 1.00 1.00 A C
+ATOM 3 CA ILE A 3 21.774 16.387 -0.280 1.00 1.00 A C
+ATOM 4 CA GLN A 4 18.856 18.298 1.245 1.00 1.00 A C
+ATOM 5 CA ASN A 5 18.857 19.202 4.845 1.00 1.00 A C
+ATOM 6 CA GLY A 6 15.658 21.079 5.005 1.00 1.00 A C
+ATOM 7 CA SER A 7 16.550 24.118 3.000 1.00 1.00 A C
+ATOM 8 CA THR A 8 20.320 24.447 3.425 1.00 1.00 A C
+ATOM 9 CA LYS A 9 21.217 22.234 0.471 1.00 1.00 A C
+ATOM 10 CA TRP A 10 24.823 21.102 0.195 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.089 18.698 -1.680 1.00 1.00 A C
+ATOM 12 CA GLN A 12 27.993 15.101 -0.654 1.00 1.00 A C
+ATOM 13 CA ASN A 13 30.244 12.749 -2.689 1.00 1.00 A C
+ATOM 14 CA GLY A 14 31.427 9.440 -1.434 1.00 1.00 A C
+ATOM 15 CA SER A 15 32.110 10.061 2.262 1.00 1.00 A C
+ATOM 16 CA THR A 16 34.894 12.557 1.844 1.00 1.00 A C
+ATOM 17 CA LYS A 17 34.023 15.552 -0.444 1.00 1.00 A C
+ATOM 18 CA ILE A 18 31.204 17.202 1.406 1.00 1.00 A C
+ATOM 19 CA TYR A 19 30.968 20.902 0.263 1.00 1.00 A C
+ATOM 20 CA THR A 20 28.911 23.272 2.228 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_20.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_20.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_20.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 23.796 12.698 -4.365 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.321 15.518 -2.381 1.00 1.00 A C
+ATOM 3 CA ILE A 3 22.098 15.635 1.428 1.00 1.00 A C
+ATOM 4 CA GLN A 4 19.542 18.422 2.115 1.00 1.00 A C
+ATOM 5 CA ASN A 5 20.160 19.757 5.751 1.00 1.00 A C
+ATOM 6 CA GLY A 6 17.413 22.395 5.776 1.00 1.00 A C
+ATOM 7 CA SER A 7 19.247 25.343 4.428 1.00 1.00 A C
+ATOM 8 CA THR A 8 22.691 23.757 4.195 1.00 1.00 A C
+ATOM 9 CA LYS A 9 23.467 22.015 1.009 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.721 18.981 0.747 1.00 1.00 A C
+ATOM 11 CA TYR A 11 26.749 17.159 -2.453 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.625 13.804 -3.014 1.00 1.00 A C
+ATOM 13 CA ASN A 13 31.458 12.325 -5.085 1.00 1.00 A C
+ATOM 14 CA GLY A 14 32.120 9.035 -3.395 1.00 1.00 A C
+ATOM 15 CA SER A 15 33.491 9.574 0.058 1.00 1.00 A C
+ATOM 16 CA THR A 16 34.191 13.320 -0.646 1.00 1.00 A C
+ATOM 17 CA LYS A 17 31.545 15.739 0.660 1.00 1.00 A C
+ATOM 18 CA ILE A 18 31.071 18.971 -1.167 1.00 1.00 A C
+ATOM 19 CA TYR A 19 29.333 21.665 0.855 1.00 1.00 A C
+ATOM 20 CA THR A 20 27.745 24.005 -1.718 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_21.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_21.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_21.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.421 12.601 -4.540 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.648 15.306 -2.629 1.00 1.00 A C
+ATOM 3 CA ILE A 3 22.135 15.373 1.245 1.00 1.00 A C
+ATOM 4 CA GLN A 4 19.769 18.186 1.742 1.00 1.00 A C
+ATOM 5 CA ASN A 5 19.623 19.863 5.158 1.00 1.00 A C
+ATOM 6 CA GLY A 6 17.847 23.215 4.417 1.00 1.00 A C
+ATOM 7 CA SER A 7 20.497 25.841 3.981 1.00 1.00 A C
+ATOM 8 CA THR A 8 23.344 23.469 4.511 1.00 1.00 A C
+ATOM 9 CA LYS A 9 23.188 21.393 1.284 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.844 18.781 1.081 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.090 17.542 -2.351 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.467 13.932 -1.707 1.00 1.00 A C
+ATOM 13 CA ASN A 13 30.910 13.427 -4.619 1.00 1.00 A C
+ATOM 14 CA GLY A 14 30.914 9.672 -3.778 1.00 1.00 A C
+ATOM 15 CA SER A 15 32.670 10.371 -0.446 1.00 1.00 A C
+ATOM 16 CA THR A 16 33.742 13.936 -0.848 1.00 1.00 A C
+ATOM 17 CA LYS A 17 31.659 16.441 1.058 1.00 1.00 A C
+ATOM 18 CA ILE A 18 31.515 19.599 -1.080 1.00 1.00 A C
+ATOM 19 CA TYR A 19 29.618 22.544 0.399 1.00 1.00 A C
+ATOM 20 CA THR A 20 26.738 23.794 -1.692 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_22.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_22.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_22.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.376 12.965 -4.657 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.753 15.275 -2.090 1.00 1.00 A C
+ATOM 3 CA ILE A 3 22.532 15.422 1.639 1.00 1.00 A C
+ATOM 4 CA GLN A 4 19.314 17.329 1.431 1.00 1.00 A C
+ATOM 5 CA ASN A 5 18.147 18.856 4.570 1.00 1.00 A C
+ATOM 6 CA GLY A 6 16.946 22.548 4.277 1.00 1.00 A C
+ATOM 7 CA SER A 7 19.836 24.976 5.005 1.00 1.00 A C
+ATOM 8 CA THR A 8 22.562 22.261 5.055 1.00 1.00 A C
+ATOM 9 CA LYS A 9 23.540 21.744 1.449 1.00 1.00 A C
+ATOM 10 CA TRP A 10 26.349 19.113 0.919 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.207 17.625 -2.490 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.853 14.265 -2.070 1.00 1.00 A C
+ATOM 13 CA ASN A 13 30.983 13.140 -4.877 1.00 1.00 A C
+ATOM 14 CA GLY A 14 31.718 9.536 -4.086 1.00 1.00 A C
+ATOM 15 CA SER A 15 33.175 9.844 -0.597 1.00 1.00 A C
+ATOM 16 CA THR A 16 34.362 13.434 -0.780 1.00 1.00 A C
+ATOM 17 CA LYS A 17 31.976 16.151 0.518 1.00 1.00 A C
+ATOM 18 CA ILE A 18 32.225 19.740 -0.588 1.00 1.00 A C
+ATOM 19 CA TYR A 19 29.792 22.514 0.032 1.00 1.00 A C
+ATOM 20 CA THR A 20 27.636 23.934 -2.835 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_23.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_23.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_23.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.493 13.118 -4.697 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.509 15.855 -2.932 1.00 1.00 A C
+ATOM 3 CA ILE A 3 21.910 15.322 0.811 1.00 1.00 A C
+ATOM 4 CA GLN A 4 19.808 18.374 1.172 1.00 1.00 A C
+ATOM 5 CA ASN A 5 18.951 19.330 4.624 1.00 1.00 A C
+ATOM 6 CA GLY A 6 17.507 22.777 4.510 1.00 1.00 A C
+ATOM 7 CA SER A 7 20.332 25.340 4.071 1.00 1.00 A C
+ATOM 8 CA THR A 8 23.114 22.651 4.514 1.00 1.00 A C
+ATOM 9 CA LYS A 9 23.399 20.943 1.123 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.953 18.205 0.895 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.104 17.381 -2.591 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.740 14.057 -1.586 1.00 1.00 A C
+ATOM 13 CA ASN A 13 30.900 12.858 -4.648 1.00 1.00 A C
+ATOM 14 CA GLY A 14 32.565 9.531 -4.033 1.00 1.00 A C
+ATOM 15 CA SER A 15 33.853 10.078 -0.619 1.00 1.00 A C
+ATOM 16 CA THR A 16 34.453 13.855 -0.363 1.00 1.00 A C
+ATOM 17 CA LYS A 17 31.540 15.997 1.100 1.00 1.00 A C
+ATOM 18 CA ILE A 18 31.327 19.374 -0.438 1.00 1.00 A C
+ATOM 19 CA TYR A 19 29.226 22.242 1.139 1.00 1.00 A C
+ATOM 20 CA THR A 20 27.063 24.177 -1.291 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_24.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_24.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_24.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.085 12.836 -4.458 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.350 15.992 -3.440 1.00 1.00 A C
+ATOM 3 CA ILE A 3 21.961 15.405 0.355 1.00 1.00 A C
+ATOM 4 CA GLN A 4 20.180 18.490 1.416 1.00 1.00 A C
+ATOM 5 CA ASN A 5 19.892 18.336 5.089 1.00 1.00 A C
+ATOM 6 CA GLY A 6 17.536 21.177 5.668 1.00 1.00 A C
+ATOM 7 CA SER A 7 19.603 24.328 5.580 1.00 1.00 A C
+ATOM 8 CA THR A 8 23.019 22.837 5.046 1.00 1.00 A C
+ATOM 9 CA LYS A 9 23.602 22.070 1.445 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.648 19.061 0.454 1.00 1.00 A C
+ATOM 11 CA TYR A 11 26.818 17.724 -2.825 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.658 14.472 -1.910 1.00 1.00 A C
+ATOM 13 CA ASN A 13 30.973 13.018 -4.601 1.00 1.00 A C
+ATOM 14 CA GLY A 14 30.525 9.504 -3.135 1.00 1.00 A C
+ATOM 15 CA SER A 15 32.914 9.633 -0.118 1.00 1.00 A C
+ATOM 16 CA THR A 16 33.980 13.409 -0.409 1.00 1.00 A C
+ATOM 17 CA LYS A 17 31.924 16.390 1.089 1.00 1.00 A C
+ATOM 18 CA ILE A 18 31.183 19.462 -1.038 1.00 1.00 A C
+ATOM 19 CA TYR A 19 29.391 22.295 0.744 1.00 1.00 A C
+ATOM 20 CA THR A 20 27.224 23.985 -1.885 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_25.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_25.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_25.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.572 13.002 -5.044 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.518 15.634 -3.182 1.00 1.00 A C
+ATOM 3 CA ILE A 3 22.316 14.930 0.518 1.00 1.00 A C
+ATOM 4 CA GLN A 4 20.540 18.272 1.285 1.00 1.00 A C
+ATOM 5 CA ASN A 5 20.853 18.805 4.953 1.00 1.00 A C
+ATOM 6 CA GLY A 6 18.238 21.607 5.519 1.00 1.00 A C
+ATOM 7 CA SER A 7 20.436 24.684 5.432 1.00 1.00 A C
+ATOM 8 CA THR A 8 23.804 22.913 4.867 1.00 1.00 A C
+ATOM 9 CA LYS A 9 23.984 21.758 1.260 1.00 1.00 A C
+ATOM 10 CA TRP A 10 26.117 18.661 1.404 1.00 1.00 A C
+ATOM 11 CA TYR A 11 26.485 17.488 -2.177 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.275 14.289 -1.620 1.00 1.00 A C
+ATOM 13 CA ASN A 13 31.040 13.578 -4.156 1.00 1.00 A C
+ATOM 14 CA GLY A 14 31.814 9.807 -3.587 1.00 1.00 A C
+ATOM 15 CA SER A 15 32.276 10.225 0.180 1.00 1.00 A C
+ATOM 16 CA THR A 16 33.897 13.671 0.660 1.00 1.00 A C
+ATOM 17 CA LYS A 17 30.862 16.111 0.682 1.00 1.00 A C
+ATOM 18 CA ILE A 18 31.403 19.264 -1.301 1.00 1.00 A C
+ATOM 19 CA TYR A 19 29.573 22.401 0.176 1.00 1.00 A C
+ATOM 20 CA THR A 20 27.180 24.108 -2.122 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_26.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_26.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_26.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 25.019 13.186 -5.011 1.00 1.00 A C
+ATOM 2 CA TRP A 2 23.011 16.125 -3.456 1.00 1.00 A C
+ATOM 3 CA ILE A 3 22.483 15.469 0.301 1.00 1.00 A C
+ATOM 4 CA GLN A 4 20.537 18.796 0.854 1.00 1.00 A C
+ATOM 5 CA ASN A 5 19.974 18.373 4.618 1.00 1.00 A C
+ATOM 6 CA GLY A 6 17.456 21.239 4.854 1.00 1.00 A C
+ATOM 7 CA SER A 7 19.700 24.127 5.811 1.00 1.00 A C
+ATOM 8 CA THR A 8 23.049 22.422 5.250 1.00 1.00 A C
+ATOM 9 CA LYS A 9 23.702 22.019 1.617 1.00 1.00 A C
+ATOM 10 CA TRP A 10 26.038 19.010 0.978 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.237 17.557 -2.264 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.810 14.118 -2.332 1.00 1.00 A C
+ATOM 13 CA ASN A 13 31.616 13.681 -4.723 1.00 1.00 A C
+ATOM 14 CA GLY A 14 31.099 10.032 -3.688 1.00 1.00 A C
+ATOM 15 CA SER A 15 32.409 9.978 -0.156 1.00 1.00 A C
+ATOM 16 CA THR A 16 33.850 13.493 -0.017 1.00 1.00 A C
+ATOM 17 CA LYS A 17 30.953 15.698 1.145 1.00 1.00 A C
+ATOM 18 CA ILE A 18 31.561 19.175 -0.061 1.00 1.00 A C
+ATOM 19 CA TYR A 19 29.577 22.139 1.131 1.00 1.00 A C
+ATOM 20 CA THR A 20 27.770 23.785 -1.691 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_27.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_27.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_27.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.555 14.516 -5.709 1.00 1.00 A C
+ATOM 2 CA TRP A 2 23.171 17.066 -3.075 1.00 1.00 A C
+ATOM 3 CA ILE A 3 22.650 15.559 0.322 1.00 1.00 A C
+ATOM 4 CA GLN A 4 20.074 17.910 1.700 1.00 1.00 A C
+ATOM 5 CA ASN A 5 20.132 17.413 5.521 1.00 1.00 A C
+ATOM 6 CA GLY A 6 16.992 19.515 6.313 1.00 1.00 A C
+ATOM 7 CA SER A 7 17.986 22.879 4.778 1.00 1.00 A C
+ATOM 8 CA THR A 8 21.695 22.161 4.274 1.00 1.00 A C
+ATOM 9 CA LYS A 9 23.446 21.047 0.928 1.00 1.00 A C
+ATOM 10 CA TRP A 10 26.356 18.741 1.240 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.385 18.015 -2.253 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.445 14.316 -2.320 1.00 1.00 A C
+ATOM 13 CA ASN A 13 31.180 13.757 -4.849 1.00 1.00 A C
+ATOM 14 CA GLY A 14 31.826 10.019 -4.374 1.00 1.00 A C
+ATOM 15 CA SER A 15 32.397 9.817 -0.563 1.00 1.00 A C
+ATOM 16 CA THR A 16 33.487 13.483 0.168 1.00 1.00 A C
+ATOM 17 CA LYS A 17 30.762 15.797 1.287 1.00 1.00 A C
+ATOM 18 CA ILE A 18 32.087 19.216 0.142 1.00 1.00 A C
+ATOM 19 CA TYR A 19 30.427 22.313 1.648 1.00 1.00 A C
+ATOM 20 CA THR A 20 28.247 23.779 -1.096 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_28.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_28.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_28.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.207 13.761 -5.087 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.516 16.479 -3.055 1.00 1.00 A C
+ATOM 3 CA ILE A 3 21.665 15.565 0.405 1.00 1.00 A C
+ATOM 4 CA GLN A 4 20.032 18.726 1.836 1.00 1.00 A C
+ATOM 5 CA ASN A 5 19.214 18.006 5.627 1.00 1.00 A C
+ATOM 6 CA GLY A 6 17.950 21.363 6.836 1.00 1.00 A C
+ATOM 7 CA SER A 7 20.399 23.950 5.825 1.00 1.00 A C
+ATOM 8 CA THR A 8 23.663 22.174 4.972 1.00 1.00 A C
+ATOM 9 CA LYS A 9 23.783 21.255 1.352 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.873 18.151 0.985 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.139 17.405 -2.572 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.743 14.080 -2.492 1.00 1.00 A C
+ATOM 13 CA ASN A 13 31.585 14.973 -4.987 1.00 1.00 A C
+ATOM 14 CA GLY A 14 32.779 11.495 -5.623 1.00 1.00 A C
+ATOM 15 CA SER A 15 32.893 10.360 -2.021 1.00 1.00 A C
+ATOM 16 CA THR A 16 33.711 13.221 0.115 1.00 1.00 A C
+ATOM 17 CA LYS A 17 30.519 14.785 1.162 1.00 1.00 A C
+ATOM 18 CA ILE A 18 31.062 18.544 0.991 1.00 1.00 A C
+ATOM 19 CA TYR A 19 29.218 21.760 1.843 1.00 1.00 A C
+ATOM 20 CA THR A 20 28.114 23.447 -1.419 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_29.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_29.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_29.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.174 13.449 -5.263 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.310 16.019 -3.247 1.00 1.00 A C
+ATOM 3 CA ILE A 3 22.355 15.309 0.557 1.00 1.00 A C
+ATOM 4 CA GLN A 4 20.318 17.917 2.075 1.00 1.00 A C
+ATOM 5 CA ASN A 5 21.637 18.647 5.559 1.00 1.00 A C
+ATOM 6 CA GLY A 6 18.650 20.228 7.265 1.00 1.00 A C
+ATOM 7 CA SER A 7 18.264 22.936 4.456 1.00 1.00 A C
+ATOM 8 CA THR A 8 21.472 23.471 2.314 1.00 1.00 A C
+ATOM 9 CA LYS A 9 22.273 20.938 -0.406 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.721 19.764 0.251 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.057 18.064 -2.762 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.201 14.438 -2.128 1.00 1.00 A C
+ATOM 13 CA ASN A 13 30.923 13.942 -4.798 1.00 1.00 A C
+ATOM 14 CA GLY A 14 31.172 10.315 -5.043 1.00 1.00 A C
+ATOM 15 CA SER A 15 31.962 9.853 -1.396 1.00 1.00 A C
+ATOM 16 CA THR A 16 33.102 13.334 -0.312 1.00 1.00 A C
+ATOM 17 CA LYS A 17 30.808 16.011 1.016 1.00 1.00 A C
+ATOM 18 CA ILE A 18 32.068 19.410 -0.005 1.00 1.00 A C
+ATOM 19 CA TYR A 19 31.835 21.896 2.934 1.00 1.00 A C
+ATOM 20 CA THR A 20 32.246 25.533 3.644 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_0.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_0.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_0.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.673 12.849 -5.563 1.00 1.00 A C
+ATOM 2 CA TRP A 2 23.214 16.010 -3.963 1.00 1.00 A C
+ATOM 3 CA ILE A 3 21.548 16.254 -0.576 1.00 1.00 A C
+ATOM 4 CA GLN A 4 20.016 19.808 -0.155 1.00 1.00 A C
+ATOM 5 CA ASN A 5 19.099 20.043 3.540 1.00 1.00 A C
+ATOM 6 CA GLY A 6 18.524 23.803 3.815 1.00 1.00 A C
+ATOM 7 CA SER A 7 21.444 25.372 5.538 1.00 1.00 A C
+ATOM 8 CA THR A 8 24.070 22.640 4.658 1.00 1.00 A C
+ATOM 9 CA LYS A 9 24.134 20.811 1.513 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.793 17.385 1.534 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.436 15.607 -1.401 1.00 1.00 A C
+ATOM 12 CA GLN A 12 27.949 11.896 -1.672 1.00 1.00 A C
+ATOM 13 CA ASN A 13 30.575 11.904 -4.260 1.00 1.00 A C
+ATOM 14 CA GLY A 14 32.990 9.317 -2.740 1.00 1.00 A C
+ATOM 15 CA SER A 15 34.181 10.934 0.395 1.00 1.00 A C
+ATOM 16 CA THR A 16 31.643 13.473 1.511 1.00 1.00 A C
+ATOM 17 CA LYS A 17 31.955 17.104 0.909 1.00 1.00 A C
+ATOM 18 CA ILE A 18 30.593 20.181 2.548 1.00 1.00 A C
+ATOM 19 CA TYR A 19 28.636 22.877 0.832 1.00 1.00 A C
+ATOM 20 CA THR A 20 26.003 25.623 1.670 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_1.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_1.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_1.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 23.546 11.933 -4.152 1.00 1.00 A C
+ATOM 2 CA TRP A 2 23.092 15.533 -3.095 1.00 1.00 A C
+ATOM 3 CA ILE A 3 21.586 16.045 0.423 1.00 1.00 A C
+ATOM 4 CA GLN A 4 19.383 19.118 -0.271 1.00 1.00 A C
+ATOM 5 CA ASN A 5 18.924 20.615 3.129 1.00 1.00 A C
+ATOM 6 CA GLY A 6 17.682 24.082 2.309 1.00 1.00 A C
+ATOM 7 CA SER A 7 20.285 25.605 0.166 1.00 1.00 A C
+ATOM 8 CA THR A 8 23.149 23.575 1.748 1.00 1.00 A C
+ATOM 9 CA LYS A 9 23.540 20.884 -0.781 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.473 18.167 1.163 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.403 16.255 -1.719 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.017 12.473 -1.486 1.00 1.00 A C
+ATOM 13 CA ASN A 13 29.157 11.132 -4.922 1.00 1.00 A C
+ATOM 14 CA GLY A 14 33.003 11.091 -5.274 1.00 1.00 A C
+ATOM 15 CA SER A 15 33.863 13.286 -2.370 1.00 1.00 A C
+ATOM 16 CA THR A 16 31.872 13.825 0.775 1.00 1.00 A C
+ATOM 17 CA LYS A 17 31.403 17.638 1.008 1.00 1.00 A C
+ATOM 18 CA ILE A 18 30.057 18.320 4.446 1.00 1.00 A C
+ATOM 19 CA TYR A 19 29.835 22.075 4.711 1.00 1.00 A C
+ATOM 20 CA THR A 20 30.651 23.250 8.229 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_10.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_10.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_10.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.419 12.685 -3.263 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.276 15.712 -2.827 1.00 1.00 A C
+ATOM 3 CA ILE A 3 21.226 16.432 0.503 1.00 1.00 A C
+ATOM 4 CA GLN A 4 18.950 19.482 1.186 1.00 1.00 A C
+ATOM 5 CA ASN A 5 19.978 20.507 4.684 1.00 1.00 A C
+ATOM 6 CA GLY A 6 17.949 23.676 4.912 1.00 1.00 A C
+ATOM 7 CA SER A 7 20.481 26.308 3.873 1.00 1.00 A C
+ATOM 8 CA THR A 8 23.516 24.060 3.804 1.00 1.00 A C
+ATOM 9 CA LYS A 9 23.314 22.350 0.393 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.297 19.185 1.008 1.00 1.00 A C
+ATOM 11 CA TYR A 11 26.810 17.848 -2.156 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.656 14.531 -1.801 1.00 1.00 A C
+ATOM 13 CA ASN A 13 30.468 12.966 -4.798 1.00 1.00 A C
+ATOM 14 CA GLY A 14 29.975 9.649 -3.202 1.00 1.00 A C
+ATOM 15 CA SER A 15 32.431 9.524 -0.294 1.00 1.00 A C
+ATOM 16 CA THR A 16 33.863 12.946 0.247 1.00 1.00 A C
+ATOM 17 CA LYS A 17 31.233 15.535 1.105 1.00 1.00 A C
+ATOM 18 CA ILE A 18 32.610 18.526 -0.756 1.00 1.00 A C
+ATOM 19 CA TYR A 19 29.870 21.300 -0.394 1.00 1.00 A C
+ATOM 20 CA THR A 20 29.756 21.993 3.370 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_11.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_11.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_11.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 23.950 12.754 -2.687 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.225 16.096 -1.947 1.00 1.00 A C
+ATOM 3 CA ILE A 3 21.865 16.333 1.807 1.00 1.00 A C
+ATOM 4 CA GLN A 4 19.133 18.680 2.451 1.00 1.00 A C
+ATOM 5 CA ASN A 5 19.492 21.524 5.006 1.00 1.00 A C
+ATOM 6 CA GLY A 6 17.493 24.579 3.882 1.00 1.00 A C
+ATOM 7 CA SER A 7 19.961 26.565 1.758 1.00 1.00 A C
+ATOM 8 CA THR A 8 23.048 24.417 2.185 1.00 1.00 A C
+ATOM 9 CA LYS A 9 22.580 21.150 0.360 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.653 19.062 0.978 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.037 17.293 -2.028 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.326 13.916 -1.140 1.00 1.00 A C
+ATOM 13 CA ASN A 13 29.714 13.147 -4.590 1.00 1.00 A C
+ATOM 14 CA GLY A 14 30.463 9.490 -4.662 1.00 1.00 A C
+ATOM 15 CA SER A 15 33.694 9.112 -2.701 1.00 1.00 A C
+ATOM 16 CA THR A 16 34.195 12.758 -1.628 1.00 1.00 A C
+ATOM 17 CA LYS A 17 32.016 15.521 -0.003 1.00 1.00 A C
+ATOM 18 CA ILE A 18 32.618 19.021 -1.280 1.00 1.00 A C
+ATOM 19 CA TYR A 19 30.441 20.995 1.106 1.00 1.00 A C
+ATOM 20 CA THR A 20 30.925 19.995 4.714 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_12.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_12.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_12.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 23.915 12.437 -2.833 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.386 15.820 -1.546 1.00 1.00 A C
+ATOM 3 CA ILE A 3 22.086 16.261 2.277 1.00 1.00 A C
+ATOM 4 CA GLN A 4 19.380 18.674 3.159 1.00 1.00 A C
+ATOM 5 CA ASN A 5 19.855 20.660 6.389 1.00 1.00 A C
+ATOM 6 CA GLY A 6 18.264 23.986 7.049 1.00 1.00 A C
+ATOM 7 CA SER A 7 18.738 25.910 3.879 1.00 1.00 A C
+ATOM 8 CA THR A 8 21.878 24.973 2.416 1.00 1.00 A C
+ATOM 9 CA LYS A 9 22.116 21.370 0.839 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.483 19.651 0.700 1.00 1.00 A C
+ATOM 11 CA TYR A 11 26.630 17.372 -2.150 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.696 14.386 -1.495 1.00 1.00 A C
+ATOM 13 CA ASN A 13 29.715 12.409 -4.568 1.00 1.00 A C
+ATOM 14 CA GLY A 14 30.319 8.879 -3.239 1.00 1.00 A C
+ATOM 15 CA SER A 15 33.683 9.250 -1.576 1.00 1.00 A C
+ATOM 16 CA THR A 16 34.923 12.834 -1.655 1.00 1.00 A C
+ATOM 17 CA LYS A 17 32.838 15.615 -0.395 1.00 1.00 A C
+ATOM 18 CA ILE A 18 32.778 18.832 -2.439 1.00 1.00 A C
+ATOM 19 CA TYR A 19 30.068 20.939 -0.775 1.00 1.00 A C
+ATOM 20 CA THR A 20 31.498 21.332 2.723 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_13.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_13.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_13.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 23.321 12.731 -3.752 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.189 16.128 -2.341 1.00 1.00 A C
+ATOM 3 CA ILE A 3 21.974 15.695 1.572 1.00 1.00 A C
+ATOM 4 CA GLN A 4 20.358 18.509 3.401 1.00 1.00 A C
+ATOM 5 CA ASN A 5 21.674 20.134 6.631 1.00 1.00 A C
+ATOM 6 CA GLY A 6 18.559 22.348 6.596 1.00 1.00 A C
+ATOM 7 CA SER A 7 18.723 24.887 3.895 1.00 1.00 A C
+ATOM 8 CA THR A 8 22.402 24.166 3.181 1.00 1.00 A C
+ATOM 9 CA LYS A 9 22.194 21.105 1.138 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.684 19.589 0.431 1.00 1.00 A C
+ATOM 11 CA TYR A 11 26.352 17.430 -2.546 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.101 14.177 -1.938 1.00 1.00 A C
+ATOM 13 CA ASN A 13 30.394 13.185 -4.838 1.00 1.00 A C
+ATOM 14 CA GLY A 14 30.278 9.509 -3.970 1.00 1.00 A C
+ATOM 15 CA SER A 15 32.400 9.405 -0.743 1.00 1.00 A C
+ATOM 16 CA THR A 16 33.550 12.957 0.242 1.00 1.00 A C
+ATOM 17 CA LYS A 17 31.086 15.777 0.326 1.00 1.00 A C
+ATOM 18 CA ILE A 18 32.309 18.411 -1.981 1.00 1.00 A C
+ATOM 19 CA TYR A 19 30.841 21.576 -0.642 1.00 1.00 A C
+ATOM 20 CA THR A 20 32.252 23.275 2.592 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_14.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_14.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_14.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.422 13.210 -4.270 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.624 15.829 -2.116 1.00 1.00 A C
+ATOM 3 CA ILE A 3 23.196 15.863 1.663 1.00 1.00 A C
+ATOM 4 CA GLN A 4 20.058 17.420 3.035 1.00 1.00 A C
+ATOM 5 CA ASN A 5 19.770 19.885 5.821 1.00 1.00 A C
+ATOM 6 CA GLY A 6 16.963 22.270 4.795 1.00 1.00 A C
+ATOM 7 CA SER A 7 19.386 25.207 5.037 1.00 1.00 A C
+ATOM 8 CA THR A 8 22.947 24.142 4.134 1.00 1.00 A C
+ATOM 9 CA LYS A 9 22.673 21.495 1.497 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.962 19.675 0.755 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.125 17.980 -2.420 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.785 14.662 -2.342 1.00 1.00 A C
+ATOM 13 CA ASN A 13 30.874 12.584 -4.720 1.00 1.00 A C
+ATOM 14 CA GLY A 14 29.992 9.290 -3.004 1.00 1.00 A C
+ATOM 15 CA SER A 15 31.881 10.055 0.268 1.00 1.00 A C
+ATOM 16 CA THR A 16 34.162 13.086 -0.326 1.00 1.00 A C
+ATOM 17 CA LYS A 17 32.466 16.502 -0.373 1.00 1.00 A C
+ATOM 18 CA ILE A 18 32.805 19.002 -3.256 1.00 1.00 A C
+ATOM 19 CA TYR A 19 30.292 21.512 -1.957 1.00 1.00 A C
+ATOM 20 CA THR A 20 30.535 22.144 1.734 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_15.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_15.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_15.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.249 12.885 -3.482 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.632 15.862 -1.801 1.00 1.00 A C
+ATOM 3 CA ILE A 3 23.160 15.596 1.871 1.00 1.00 A C
+ATOM 4 CA GLN A 4 20.481 17.553 3.855 1.00 1.00 A C
+ATOM 5 CA ASN A 5 20.622 18.794 7.522 1.00 1.00 A C
+ATOM 6 CA GLY A 6 17.047 20.185 7.631 1.00 1.00 A C
+ATOM 7 CA SER A 7 17.652 23.644 6.004 1.00 1.00 A C
+ATOM 8 CA THR A 8 21.142 22.976 4.870 1.00 1.00 A C
+ATOM 9 CA LYS A 9 22.224 21.392 1.674 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.807 19.948 1.006 1.00 1.00 A C
+ATOM 11 CA TYR A 11 26.890 18.154 -2.137 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.612 14.763 -2.258 1.00 1.00 A C
+ATOM 13 CA ASN A 13 30.363 13.522 -5.358 1.00 1.00 A C
+ATOM 14 CA GLY A 14 30.821 9.837 -4.897 1.00 1.00 A C
+ATOM 15 CA SER A 15 32.075 9.710 -1.313 1.00 1.00 A C
+ATOM 16 CA THR A 16 33.161 13.055 0.193 1.00 1.00 A C
+ATOM 17 CA LYS A 17 31.680 16.401 0.674 1.00 1.00 A C
+ATOM 18 CA ILE A 18 32.952 19.269 -1.331 1.00 1.00 A C
+ATOM 19 CA TYR A 19 30.315 21.875 -2.402 1.00 1.00 A C
+ATOM 20 CA THR A 20 28.564 24.563 -0.415 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_16.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_16.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_16.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 23.974 12.646 -3.769 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.405 15.755 -2.083 1.00 1.00 A C
+ATOM 3 CA ILE A 3 22.693 15.783 1.678 1.00 1.00 A C
+ATOM 4 CA GLN A 4 20.617 18.789 2.532 1.00 1.00 A C
+ATOM 5 CA ASN A 5 20.339 19.250 6.352 1.00 1.00 A C
+ATOM 6 CA GLY A 6 18.218 21.978 7.807 1.00 1.00 A C
+ATOM 7 CA SER A 7 19.448 24.513 5.234 1.00 1.00 A C
+ATOM 8 CA THR A 8 22.971 23.244 4.508 1.00 1.00 A C
+ATOM 9 CA LYS A 9 23.438 21.510 1.236 1.00 1.00 A C
+ATOM 10 CA TRP A 10 26.523 19.434 0.960 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.193 17.309 -2.223 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.595 13.899 -2.045 1.00 1.00 A C
+ATOM 13 CA ASN A 13 30.657 13.367 -5.167 1.00 1.00 A C
+ATOM 14 CA GLY A 14 31.134 9.682 -4.332 1.00 1.00 A C
+ATOM 15 CA SER A 15 32.411 9.712 -0.758 1.00 1.00 A C
+ATOM 16 CA THR A 16 33.605 13.262 -0.309 1.00 1.00 A C
+ATOM 17 CA LYS A 17 31.182 15.927 0.608 1.00 1.00 A C
+ATOM 18 CA ILE A 18 31.794 19.283 -1.201 1.00 1.00 A C
+ATOM 19 CA TYR A 19 29.858 22.455 -0.484 1.00 1.00 A C
+ATOM 20 CA THR A 20 27.716 23.614 -3.365 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_17.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_17.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_17.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 23.994 12.669 -4.114 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.205 15.504 -2.590 1.00 1.00 A C
+ATOM 3 CA ILE A 3 22.559 15.626 1.193 1.00 1.00 A C
+ATOM 4 CA GLN A 4 19.754 18.051 1.930 1.00 1.00 A C
+ATOM 5 CA ASN A 5 19.998 19.217 5.493 1.00 1.00 A C
+ATOM 6 CA GLY A 6 17.487 21.861 5.194 1.00 1.00 A C
+ATOM 7 CA SER A 7 19.728 24.996 4.967 1.00 1.00 A C
+ATOM 8 CA THR A 8 23.338 23.453 5.222 1.00 1.00 A C
+ATOM 9 CA LYS A 9 23.152 21.149 2.408 1.00 1.00 A C
+ATOM 10 CA TRP A 10 26.287 19.339 0.930 1.00 1.00 A C
+ATOM 11 CA TYR A 11 26.894 17.702 -2.411 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.429 14.246 -2.174 1.00 1.00 A C
+ATOM 13 CA ASN A 13 31.096 13.695 -4.735 1.00 1.00 A C
+ATOM 14 CA GLY A 14 31.045 9.948 -4.411 1.00 1.00 A C
+ATOM 15 CA SER A 15 33.058 9.644 -1.217 1.00 1.00 A C
+ATOM 16 CA THR A 16 33.804 13.308 -0.388 1.00 1.00 A C
+ATOM 17 CA LYS A 17 31.001 15.374 1.058 1.00 1.00 A C
+ATOM 18 CA ILE A 18 31.678 18.928 0.193 1.00 1.00 A C
+ATOM 19 CA TYR A 19 29.936 22.295 -0.013 1.00 1.00 A C
+ATOM 20 CA THR A 20 29.753 23.181 -3.710 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_18.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_18.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_18.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.215 12.473 -4.133 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.396 15.422 -2.396 1.00 1.00 A C
+ATOM 3 CA ILE A 3 22.572 15.614 1.424 1.00 1.00 A C
+ATOM 4 CA GLN A 4 20.158 18.403 2.196 1.00 1.00 A C
+ATOM 5 CA ASN A 5 19.425 19.100 5.826 1.00 1.00 A C
+ATOM 6 CA GLY A 6 16.946 21.960 5.760 1.00 1.00 A C
+ATOM 7 CA SER A 7 19.332 25.036 5.613 1.00 1.00 A C
+ATOM 8 CA THR A 8 22.638 23.196 5.183 1.00 1.00 A C
+ATOM 9 CA LYS A 9 22.996 21.704 1.767 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.821 19.583 0.465 1.00 1.00 A C
+ATOM 11 CA TYR A 11 26.899 17.351 -2.415 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.541 14.014 -2.054 1.00 1.00 A C
+ATOM 13 CA ASN A 13 30.636 13.738 -5.155 1.00 1.00 A C
+ATOM 14 CA GLY A 14 31.084 10.047 -4.798 1.00 1.00 A C
+ATOM 15 CA SER A 15 33.402 9.701 -1.822 1.00 1.00 A C
+ATOM 16 CA THR A 16 34.217 13.328 -0.984 1.00 1.00 A C
+ATOM 17 CA LYS A 17 31.736 15.865 0.674 1.00 1.00 A C
+ATOM 18 CA ILE A 18 31.492 19.195 -1.052 1.00 1.00 A C
+ATOM 19 CA TYR A 19 29.853 22.519 0.083 1.00 1.00 A C
+ATOM 20 CA THR A 20 27.113 23.654 -2.460 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_19.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_19.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_19.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.425 12.824 -3.856 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.623 15.909 -2.416 1.00 1.00 A C
+ATOM 3 CA ILE A 3 22.456 15.514 1.338 1.00 1.00 A C
+ATOM 4 CA GLN A 4 19.671 17.868 2.550 1.00 1.00 A C
+ATOM 5 CA ASN A 5 19.525 19.046 6.053 1.00 1.00 A C
+ATOM 6 CA GLY A 6 17.165 21.897 6.317 1.00 1.00 A C
+ATOM 7 CA SER A 7 18.676 24.410 3.980 1.00 1.00 A C
+ATOM 8 CA THR A 8 22.359 23.490 3.771 1.00 1.00 A C
+ATOM 9 CA LYS A 9 22.869 20.925 1.087 1.00 1.00 A C
+ATOM 10 CA TRP A 10 26.241 19.231 0.929 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.373 17.821 -2.507 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.673 14.261 -2.089 1.00 1.00 A C
+ATOM 13 CA ASN A 13 30.929 12.848 -4.773 1.00 1.00 A C
+ATOM 14 CA GLY A 14 31.377 9.667 -2.959 1.00 1.00 A C
+ATOM 15 CA SER A 15 33.926 10.130 -0.373 1.00 1.00 A C
+ATOM 16 CA THR A 16 34.390 13.832 -0.730 1.00 1.00 A C
+ATOM 17 CA LYS A 17 31.886 16.587 0.129 1.00 1.00 A C
+ATOM 18 CA ILE A 18 31.398 20.060 -1.263 1.00 1.00 A C
+ATOM 19 CA TYR A 19 29.572 22.709 0.941 1.00 1.00 A C
+ATOM 20 CA THR A 20 27.090 23.804 -1.765 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_2.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_2.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_2.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.961 14.402 -5.078 1.00 1.00 A C
+ATOM 2 CA TRP A 2 23.326 17.516 -3.560 1.00 1.00 A C
+ATOM 3 CA ILE A 3 21.774 16.387 -0.280 1.00 1.00 A C
+ATOM 4 CA GLN A 4 18.856 18.298 1.245 1.00 1.00 A C
+ATOM 5 CA ASN A 5 18.857 19.202 4.845 1.00 1.00 A C
+ATOM 6 CA GLY A 6 15.658 21.079 5.005 1.00 1.00 A C
+ATOM 7 CA SER A 7 16.550 24.118 3.000 1.00 1.00 A C
+ATOM 8 CA THR A 8 20.320 24.447 3.425 1.00 1.00 A C
+ATOM 9 CA LYS A 9 21.217 22.234 0.471 1.00 1.00 A C
+ATOM 10 CA TRP A 10 24.823 21.102 0.195 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.089 18.698 -1.680 1.00 1.00 A C
+ATOM 12 CA GLN A 12 27.993 15.101 -0.654 1.00 1.00 A C
+ATOM 13 CA ASN A 13 30.244 12.749 -2.689 1.00 1.00 A C
+ATOM 14 CA GLY A 14 31.427 9.440 -1.434 1.00 1.00 A C
+ATOM 15 CA SER A 15 32.110 10.061 2.262 1.00 1.00 A C
+ATOM 16 CA THR A 16 34.894 12.557 1.844 1.00 1.00 A C
+ATOM 17 CA LYS A 17 34.023 15.552 -0.444 1.00 1.00 A C
+ATOM 18 CA ILE A 18 31.204 17.202 1.406 1.00 1.00 A C
+ATOM 19 CA TYR A 19 30.968 20.902 0.263 1.00 1.00 A C
+ATOM 20 CA THR A 20 28.911 23.272 2.228 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_20.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_20.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_20.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 23.796 12.698 -4.365 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.321 15.518 -2.381 1.00 1.00 A C
+ATOM 3 CA ILE A 3 22.098 15.635 1.428 1.00 1.00 A C
+ATOM 4 CA GLN A 4 19.542 18.422 2.115 1.00 1.00 A C
+ATOM 5 CA ASN A 5 20.160 19.757 5.751 1.00 1.00 A C
+ATOM 6 CA GLY A 6 17.413 22.395 5.776 1.00 1.00 A C
+ATOM 7 CA SER A 7 19.247 25.343 4.428 1.00 1.00 A C
+ATOM 8 CA THR A 8 22.691 23.757 4.195 1.00 1.00 A C
+ATOM 9 CA LYS A 9 23.467 22.015 1.009 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.721 18.981 0.747 1.00 1.00 A C
+ATOM 11 CA TYR A 11 26.749 17.159 -2.453 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.625 13.804 -3.014 1.00 1.00 A C
+ATOM 13 CA ASN A 13 31.458 12.325 -5.085 1.00 1.00 A C
+ATOM 14 CA GLY A 14 32.120 9.035 -3.395 1.00 1.00 A C
+ATOM 15 CA SER A 15 33.491 9.574 0.058 1.00 1.00 A C
+ATOM 16 CA THR A 16 34.191 13.320 -0.646 1.00 1.00 A C
+ATOM 17 CA LYS A 17 31.545 15.739 0.660 1.00 1.00 A C
+ATOM 18 CA ILE A 18 31.071 18.971 -1.167 1.00 1.00 A C
+ATOM 19 CA TYR A 19 29.333 21.665 0.855 1.00 1.00 A C
+ATOM 20 CA THR A 20 27.745 24.005 -1.718 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_21.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_21.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_21.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.421 12.601 -4.540 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.648 15.306 -2.629 1.00 1.00 A C
+ATOM 3 CA ILE A 3 22.135 15.373 1.245 1.00 1.00 A C
+ATOM 4 CA GLN A 4 19.769 18.186 1.742 1.00 1.00 A C
+ATOM 5 CA ASN A 5 19.623 19.863 5.158 1.00 1.00 A C
+ATOM 6 CA GLY A 6 17.847 23.215 4.417 1.00 1.00 A C
+ATOM 7 CA SER A 7 20.497 25.841 3.981 1.00 1.00 A C
+ATOM 8 CA THR A 8 23.344 23.469 4.511 1.00 1.00 A C
+ATOM 9 CA LYS A 9 23.188 21.393 1.284 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.844 18.781 1.081 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.090 17.542 -2.351 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.467 13.932 -1.707 1.00 1.00 A C
+ATOM 13 CA ASN A 13 30.910 13.427 -4.619 1.00 1.00 A C
+ATOM 14 CA GLY A 14 30.914 9.672 -3.778 1.00 1.00 A C
+ATOM 15 CA SER A 15 32.670 10.371 -0.446 1.00 1.00 A C
+ATOM 16 CA THR A 16 33.742 13.936 -0.848 1.00 1.00 A C
+ATOM 17 CA LYS A 17 31.659 16.441 1.058 1.00 1.00 A C
+ATOM 18 CA ILE A 18 31.515 19.599 -1.080 1.00 1.00 A C
+ATOM 19 CA TYR A 19 29.618 22.544 0.399 1.00 1.00 A C
+ATOM 20 CA THR A 20 26.738 23.794 -1.692 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_22.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_22.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_22.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.376 12.965 -4.657 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.753 15.275 -2.090 1.00 1.00 A C
+ATOM 3 CA ILE A 3 22.532 15.422 1.639 1.00 1.00 A C
+ATOM 4 CA GLN A 4 19.314 17.329 1.431 1.00 1.00 A C
+ATOM 5 CA ASN A 5 18.147 18.856 4.570 1.00 1.00 A C
+ATOM 6 CA GLY A 6 16.946 22.548 4.277 1.00 1.00 A C
+ATOM 7 CA SER A 7 19.836 24.976 5.005 1.00 1.00 A C
+ATOM 8 CA THR A 8 22.562 22.261 5.055 1.00 1.00 A C
+ATOM 9 CA LYS A 9 23.540 21.744 1.449 1.00 1.00 A C
+ATOM 10 CA TRP A 10 26.349 19.113 0.919 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.207 17.625 -2.490 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.853 14.265 -2.070 1.00 1.00 A C
+ATOM 13 CA ASN A 13 30.983 13.140 -4.877 1.00 1.00 A C
+ATOM 14 CA GLY A 14 31.718 9.536 -4.086 1.00 1.00 A C
+ATOM 15 CA SER A 15 33.175 9.844 -0.597 1.00 1.00 A C
+ATOM 16 CA THR A 16 34.362 13.434 -0.780 1.00 1.00 A C
+ATOM 17 CA LYS A 17 31.976 16.151 0.518 1.00 1.00 A C
+ATOM 18 CA ILE A 18 32.225 19.740 -0.588 1.00 1.00 A C
+ATOM 19 CA TYR A 19 29.792 22.514 0.032 1.00 1.00 A C
+ATOM 20 CA THR A 20 27.636 23.934 -2.835 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_23.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_23.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_23.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.493 13.118 -4.697 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.509 15.855 -2.932 1.00 1.00 A C
+ATOM 3 CA ILE A 3 21.910 15.322 0.811 1.00 1.00 A C
+ATOM 4 CA GLN A 4 19.808 18.374 1.172 1.00 1.00 A C
+ATOM 5 CA ASN A 5 18.951 19.330 4.624 1.00 1.00 A C
+ATOM 6 CA GLY A 6 17.507 22.777 4.510 1.00 1.00 A C
+ATOM 7 CA SER A 7 20.332 25.340 4.071 1.00 1.00 A C
+ATOM 8 CA THR A 8 23.114 22.651 4.514 1.00 1.00 A C
+ATOM 9 CA LYS A 9 23.399 20.943 1.123 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.953 18.205 0.895 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.104 17.381 -2.591 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.740 14.057 -1.586 1.00 1.00 A C
+ATOM 13 CA ASN A 13 30.900 12.858 -4.648 1.00 1.00 A C
+ATOM 14 CA GLY A 14 32.565 9.531 -4.033 1.00 1.00 A C
+ATOM 15 CA SER A 15 33.853 10.078 -0.619 1.00 1.00 A C
+ATOM 16 CA THR A 16 34.453 13.855 -0.363 1.00 1.00 A C
+ATOM 17 CA LYS A 17 31.540 15.997 1.100 1.00 1.00 A C
+ATOM 18 CA ILE A 18 31.327 19.374 -0.438 1.00 1.00 A C
+ATOM 19 CA TYR A 19 29.226 22.242 1.139 1.00 1.00 A C
+ATOM 20 CA THR A 20 27.063 24.177 -1.291 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_24.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_24.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_24.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.085 12.836 -4.458 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.350 15.992 -3.440 1.00 1.00 A C
+ATOM 3 CA ILE A 3 21.961 15.405 0.355 1.00 1.00 A C
+ATOM 4 CA GLN A 4 20.180 18.490 1.416 1.00 1.00 A C
+ATOM 5 CA ASN A 5 19.892 18.336 5.089 1.00 1.00 A C
+ATOM 6 CA GLY A 6 17.536 21.177 5.668 1.00 1.00 A C
+ATOM 7 CA SER A 7 19.603 24.328 5.580 1.00 1.00 A C
+ATOM 8 CA THR A 8 23.019 22.837 5.046 1.00 1.00 A C
+ATOM 9 CA LYS A 9 23.602 22.070 1.445 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.648 19.061 0.454 1.00 1.00 A C
+ATOM 11 CA TYR A 11 26.818 17.724 -2.825 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.658 14.472 -1.910 1.00 1.00 A C
+ATOM 13 CA ASN A 13 30.973 13.018 -4.601 1.00 1.00 A C
+ATOM 14 CA GLY A 14 30.525 9.504 -3.135 1.00 1.00 A C
+ATOM 15 CA SER A 15 32.914 9.633 -0.118 1.00 1.00 A C
+ATOM 16 CA THR A 16 33.980 13.409 -0.409 1.00 1.00 A C
+ATOM 17 CA LYS A 17 31.924 16.390 1.089 1.00 1.00 A C
+ATOM 18 CA ILE A 18 31.183 19.462 -1.038 1.00 1.00 A C
+ATOM 19 CA TYR A 19 29.391 22.295 0.744 1.00 1.00 A C
+ATOM 20 CA THR A 20 27.224 23.985 -1.885 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_25.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_25.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_25.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.572 13.002 -5.044 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.518 15.634 -3.182 1.00 1.00 A C
+ATOM 3 CA ILE A 3 22.316 14.930 0.518 1.00 1.00 A C
+ATOM 4 CA GLN A 4 20.540 18.272 1.285 1.00 1.00 A C
+ATOM 5 CA ASN A 5 20.853 18.805 4.953 1.00 1.00 A C
+ATOM 6 CA GLY A 6 18.238 21.607 5.519 1.00 1.00 A C
+ATOM 7 CA SER A 7 20.436 24.684 5.432 1.00 1.00 A C
+ATOM 8 CA THR A 8 23.804 22.913 4.867 1.00 1.00 A C
+ATOM 9 CA LYS A 9 23.984 21.758 1.260 1.00 1.00 A C
+ATOM 10 CA TRP A 10 26.117 18.661 1.404 1.00 1.00 A C
+ATOM 11 CA TYR A 11 26.485 17.488 -2.177 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.275 14.289 -1.620 1.00 1.00 A C
+ATOM 13 CA ASN A 13 31.040 13.578 -4.156 1.00 1.00 A C
+ATOM 14 CA GLY A 14 31.814 9.807 -3.587 1.00 1.00 A C
+ATOM 15 CA SER A 15 32.276 10.225 0.180 1.00 1.00 A C
+ATOM 16 CA THR A 16 33.897 13.671 0.660 1.00 1.00 A C
+ATOM 17 CA LYS A 17 30.862 16.111 0.682 1.00 1.00 A C
+ATOM 18 CA ILE A 18 31.403 19.264 -1.301 1.00 1.00 A C
+ATOM 19 CA TYR A 19 29.573 22.401 0.176 1.00 1.00 A C
+ATOM 20 CA THR A 20 27.180 24.108 -2.122 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_26.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_26.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_26.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 25.019 13.186 -5.011 1.00 1.00 A C
+ATOM 2 CA TRP A 2 23.011 16.125 -3.456 1.00 1.00 A C
+ATOM 3 CA ILE A 3 22.483 15.469 0.301 1.00 1.00 A C
+ATOM 4 CA GLN A 4 20.537 18.796 0.854 1.00 1.00 A C
+ATOM 5 CA ASN A 5 19.974 18.373 4.618 1.00 1.00 A C
+ATOM 6 CA GLY A 6 17.456 21.239 4.854 1.00 1.00 A C
+ATOM 7 CA SER A 7 19.700 24.127 5.811 1.00 1.00 A C
+ATOM 8 CA THR A 8 23.049 22.422 5.250 1.00 1.00 A C
+ATOM 9 CA LYS A 9 23.702 22.019 1.617 1.00 1.00 A C
+ATOM 10 CA TRP A 10 26.038 19.010 0.978 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.237 17.557 -2.264 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.810 14.118 -2.332 1.00 1.00 A C
+ATOM 13 CA ASN A 13 31.616 13.681 -4.723 1.00 1.00 A C
+ATOM 14 CA GLY A 14 31.099 10.032 -3.688 1.00 1.00 A C
+ATOM 15 CA SER A 15 32.409 9.978 -0.156 1.00 1.00 A C
+ATOM 16 CA THR A 16 33.850 13.493 -0.017 1.00 1.00 A C
+ATOM 17 CA LYS A 17 30.953 15.698 1.145 1.00 1.00 A C
+ATOM 18 CA ILE A 18 31.561 19.175 -0.061 1.00 1.00 A C
+ATOM 19 CA TYR A 19 29.577 22.139 1.131 1.00 1.00 A C
+ATOM 20 CA THR A 20 27.770 23.785 -1.691 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_27.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_27.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_27.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.555 14.516 -5.709 1.00 1.00 A C
+ATOM 2 CA TRP A 2 23.171 17.066 -3.075 1.00 1.00 A C
+ATOM 3 CA ILE A 3 22.650 15.559 0.322 1.00 1.00 A C
+ATOM 4 CA GLN A 4 20.074 17.910 1.700 1.00 1.00 A C
+ATOM 5 CA ASN A 5 20.132 17.413 5.521 1.00 1.00 A C
+ATOM 6 CA GLY A 6 16.992 19.515 6.313 1.00 1.00 A C
+ATOM 7 CA SER A 7 17.986 22.879 4.778 1.00 1.00 A C
+ATOM 8 CA THR A 8 21.695 22.161 4.274 1.00 1.00 A C
+ATOM 9 CA LYS A 9 23.446 21.047 0.928 1.00 1.00 A C
+ATOM 10 CA TRP A 10 26.356 18.741 1.240 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.385 18.015 -2.253 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.445 14.316 -2.320 1.00 1.00 A C
+ATOM 13 CA ASN A 13 31.180 13.757 -4.849 1.00 1.00 A C
+ATOM 14 CA GLY A 14 31.826 10.019 -4.374 1.00 1.00 A C
+ATOM 15 CA SER A 15 32.397 9.817 -0.563 1.00 1.00 A C
+ATOM 16 CA THR A 16 33.487 13.483 0.168 1.00 1.00 A C
+ATOM 17 CA LYS A 17 30.762 15.797 1.287 1.00 1.00 A C
+ATOM 18 CA ILE A 18 32.087 19.216 0.142 1.00 1.00 A C
+ATOM 19 CA TYR A 19 30.427 22.313 1.648 1.00 1.00 A C
+ATOM 20 CA THR A 20 28.247 23.779 -1.096 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_28.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_28.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_28.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.207 13.761 -5.087 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.516 16.479 -3.055 1.00 1.00 A C
+ATOM 3 CA ILE A 3 21.665 15.565 0.405 1.00 1.00 A C
+ATOM 4 CA GLN A 4 20.032 18.726 1.836 1.00 1.00 A C
+ATOM 5 CA ASN A 5 19.214 18.006 5.627 1.00 1.00 A C
+ATOM 6 CA GLY A 6 17.950 21.363 6.836 1.00 1.00 A C
+ATOM 7 CA SER A 7 20.399 23.950 5.825 1.00 1.00 A C
+ATOM 8 CA THR A 8 23.663 22.174 4.972 1.00 1.00 A C
+ATOM 9 CA LYS A 9 23.783 21.255 1.352 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.873 18.151 0.985 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.139 17.405 -2.572 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.743 14.080 -2.492 1.00 1.00 A C
+ATOM 13 CA ASN A 13 31.585 14.973 -4.987 1.00 1.00 A C
+ATOM 14 CA GLY A 14 32.779 11.495 -5.623 1.00 1.00 A C
+ATOM 15 CA SER A 15 32.893 10.360 -2.021 1.00 1.00 A C
+ATOM 16 CA THR A 16 33.711 13.221 0.115 1.00 1.00 A C
+ATOM 17 CA LYS A 17 30.519 14.785 1.162 1.00 1.00 A C
+ATOM 18 CA ILE A 18 31.062 18.544 0.991 1.00 1.00 A C
+ATOM 19 CA TYR A 19 29.218 21.760 1.843 1.00 1.00 A C
+ATOM 20 CA THR A 20 28.114 23.447 -1.419 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_29.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_29.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_29.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.174 13.449 -5.263 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.310 16.019 -3.247 1.00 1.00 A C
+ATOM 3 CA ILE A 3 22.355 15.309 0.557 1.00 1.00 A C
+ATOM 4 CA GLN A 4 20.318 17.917 2.075 1.00 1.00 A C
+ATOM 5 CA ASN A 5 21.637 18.647 5.559 1.00 1.00 A C
+ATOM 6 CA GLY A 6 18.650 20.228 7.265 1.00 1.00 A C
+ATOM 7 CA SER A 7 18.264 22.936 4.456 1.00 1.00 A C
+ATOM 8 CA THR A 8 21.472 23.471 2.314 1.00 1.00 A C
+ATOM 9 CA LYS A 9 22.273 20.938 -0.406 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.721 19.764 0.251 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.057 18.064 -2.762 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.201 14.438 -2.128 1.00 1.00 A C
+ATOM 13 CA ASN A 13 30.923 13.942 -4.798 1.00 1.00 A C
+ATOM 14 CA GLY A 14 31.172 10.315 -5.043 1.00 1.00 A C
+ATOM 15 CA SER A 15 31.962 9.853 -1.396 1.00 1.00 A C
+ATOM 16 CA THR A 16 33.102 13.334 -0.312 1.00 1.00 A C
+ATOM 17 CA LYS A 17 30.808 16.011 1.016 1.00 1.00 A C
+ATOM 18 CA ILE A 18 32.068 19.410 -0.005 1.00 1.00 A C
+ATOM 19 CA TYR A 19 31.835 21.896 2.934 1.00 1.00 A C
+ATOM 20 CA THR A 20 32.246 25.533 3.644 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_3.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_3.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_3.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.509 14.166 -4.920 1.00 1.00 A C
+ATOM 2 CA TRP A 2 23.078 17.478 -3.578 1.00 1.00 A C
+ATOM 3 CA ILE A 3 21.301 16.616 -0.282 1.00 1.00 A C
+ATOM 4 CA GLN A 4 19.076 19.523 0.855 1.00 1.00 A C
+ATOM 5 CA ASN A 5 17.626 19.836 4.335 1.00 1.00 A C
+ATOM 6 CA GLY A 6 15.313 22.718 4.099 1.00 1.00 A C
+ATOM 7 CA SER A 7 18.087 25.363 3.755 1.00 1.00 A C
+ATOM 8 CA THR A 8 21.252 23.410 4.694 1.00 1.00 A C
+ATOM 9 CA LYS A 9 23.113 21.649 1.888 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.888 19.200 1.199 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.444 17.516 -1.902 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.305 13.984 -1.196 1.00 1.00 A C
+ATOM 13 CA ASN A 13 31.434 13.220 -2.888 1.00 1.00 A C
+ATOM 14 CA GLY A 14 33.190 9.944 -2.608 1.00 1.00 A C
+ATOM 15 CA SER A 15 32.328 9.473 1.051 1.00 1.00 A C
+ATOM 16 CA THR A 16 33.877 11.973 3.551 1.00 1.00 A C
+ATOM 17 CA LYS A 17 34.292 14.764 0.954 1.00 1.00 A C
+ATOM 18 CA ILE A 18 31.507 17.086 1.720 1.00 1.00 A C
+ATOM 19 CA TYR A 19 31.041 20.138 -0.512 1.00 1.00 A C
+ATOM 20 CA THR A 20 28.639 23.120 -0.025 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_30.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_30.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_30.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.242 15.123 -6.583 1.00 1.00 A C
+ATOM 2 CA TRP A 2 23.126 17.647 -4.049 1.00 1.00 A C
+ATOM 3 CA ILE A 3 21.682 16.066 -0.906 1.00 1.00 A C
+ATOM 4 CA GLN A 4 20.084 18.106 1.915 1.00 1.00 A C
+ATOM 5 CA ASN A 5 21.516 17.264 5.428 1.00 1.00 A C
+ATOM 6 CA GLY A 6 20.933 19.637 8.231 1.00 1.00 A C
+ATOM 7 CA SER A 7 20.613 23.146 6.613 1.00 1.00 A C
+ATOM 8 CA THR A 8 21.517 23.346 2.854 1.00 1.00 A C
+ATOM 9 CA LYS A 9 22.391 20.888 0.071 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.787 19.528 0.173 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.392 17.861 -2.782 1.00 1.00 A C
+ATOM 12 CA GLN A 12 27.936 14.222 -2.463 1.00 1.00 A C
+ATOM 13 CA ASN A 13 31.341 13.404 -3.936 1.00 1.00 A C
+ATOM 14 CA GLY A 14 31.308 9.709 -3.109 1.00 1.00 A C
+ATOM 15 CA SER A 15 32.163 9.761 0.667 1.00 1.00 A C
+ATOM 16 CA THR A 16 32.888 13.419 1.328 1.00 1.00 A C
+ATOM 17 CA LYS A 17 30.233 16.085 1.266 1.00 1.00 A C
+ATOM 18 CA ILE A 18 31.446 18.988 -0.629 1.00 1.00 A C
+ATOM 19 CA TYR A 19 29.934 21.799 1.390 1.00 1.00 A C
+ATOM 20 CA THR A 20 28.276 24.393 -1.043 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_31.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_31.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_31.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.970 13.268 -5.417 1.00 1.00 A C
+ATOM 2 CA TRP A 2 23.288 16.402 -4.056 1.00 1.00 A C
+ATOM 3 CA ILE A 3 21.657 15.735 -0.612 1.00 1.00 A C
+ATOM 4 CA GLN A 4 19.362 18.487 0.537 1.00 1.00 A C
+ATOM 5 CA ASN A 5 19.144 18.356 4.364 1.00 1.00 A C
+ATOM 6 CA GLY A 6 17.210 21.531 4.872 1.00 1.00 A C
+ATOM 7 CA SER A 7 19.783 24.421 4.998 1.00 1.00 A C
+ATOM 8 CA THR A 8 22.769 22.072 5.026 1.00 1.00 A C
+ATOM 9 CA LYS A 9 23.243 21.634 1.271 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.808 18.848 0.383 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.359 17.883 -2.804 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.609 14.455 -1.949 1.00 1.00 A C
+ATOM 13 CA ASN A 13 31.043 13.342 -4.609 1.00 1.00 A C
+ATOM 14 CA GLY A 14 31.123 9.761 -3.209 1.00 1.00 A C
+ATOM 15 CA SER A 15 32.993 10.346 -0.004 1.00 1.00 A C
+ATOM 16 CA THR A 16 33.964 14.041 -0.444 1.00 1.00 A C
+ATOM 17 CA LYS A 17 31.355 16.403 1.001 1.00 1.00 A C
+ATOM 18 CA ILE A 18 31.209 19.890 -0.638 1.00 1.00 A C
+ATOM 19 CA TYR A 19 29.567 22.455 1.634 1.00 1.00 A C
+ATOM 20 CA THR A 20 27.508 24.566 -0.592 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_4.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_4.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_4.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 25.693 13.770 -4.875 1.00 1.00 A C
+ATOM 2 CA TRP A 2 23.228 16.580 -4.231 1.00 1.00 A C
+ATOM 3 CA ILE A 3 22.236 16.463 -0.650 1.00 1.00 A C
+ATOM 4 CA GLN A 4 19.794 18.333 1.448 1.00 1.00 A C
+ATOM 5 CA ASN A 5 19.049 18.009 5.136 1.00 1.00 A C
+ATOM 6 CA GLY A 6 16.419 20.659 6.079 1.00 1.00 A C
+ATOM 7 CA SER A 7 16.240 23.900 4.201 1.00 1.00 A C
+ATOM 8 CA THR A 8 19.828 24.062 3.008 1.00 1.00 A C
+ATOM 9 CA LYS A 9 21.369 22.723 -0.153 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.028 21.733 -0.048 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.079 19.324 -2.216 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.731 15.977 -1.474 1.00 1.00 A C
+ATOM 13 CA ASN A 13 31.767 14.428 -3.209 1.00 1.00 A C
+ATOM 14 CA GLY A 14 30.007 11.198 -3.651 1.00 1.00 A C
+ATOM 15 CA SER A 15 29.241 9.859 -0.240 1.00 1.00 A C
+ATOM 16 CA THR A 16 32.514 11.279 1.300 1.00 1.00 A C
+ATOM 17 CA LYS A 17 33.671 14.853 1.409 1.00 1.00 A C
+ATOM 18 CA ILE A 18 31.276 17.586 2.246 1.00 1.00 A C
+ATOM 19 CA TYR A 19 31.304 20.869 0.273 1.00 1.00 A C
+ATOM 20 CA THR A 20 29.466 23.386 2.612 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_5.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_5.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_5.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.354 13.682 -3.743 1.00 1.00 A C
+ATOM 2 CA TRP A 2 23.172 17.338 -4.179 1.00 1.00 A C
+ATOM 3 CA ILE A 3 21.997 16.774 -0.851 1.00 1.00 A C
+ATOM 4 CA GLN A 4 19.412 18.905 0.748 1.00 1.00 A C
+ATOM 5 CA ASN A 5 19.214 18.564 4.550 1.00 1.00 A C
+ATOM 6 CA GLY A 6 15.997 20.100 5.704 1.00 1.00 A C
+ATOM 7 CA SER A 7 16.517 23.713 4.908 1.00 1.00 A C
+ATOM 8 CA THR A 8 20.118 23.883 3.679 1.00 1.00 A C
+ATOM 9 CA LYS A 9 21.506 22.283 0.476 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.006 21.015 -0.140 1.00 1.00 A C
+ATOM 11 CA TYR A 11 26.847 18.360 -2.163 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.389 14.919 -1.138 1.00 1.00 A C
+ATOM 13 CA ASN A 13 31.130 13.502 -3.394 1.00 1.00 A C
+ATOM 14 CA GLY A 14 32.022 9.924 -2.756 1.00 1.00 A C
+ATOM 15 CA SER A 15 31.032 9.386 0.897 1.00 1.00 A C
+ATOM 16 CA THR A 16 33.762 11.643 2.218 1.00 1.00 A C
+ATOM 17 CA LYS A 17 33.747 15.072 0.560 1.00 1.00 A C
+ATOM 18 CA ILE A 18 31.016 17.265 2.143 1.00 1.00 A C
+ATOM 19 CA TYR A 19 31.076 20.325 -0.073 1.00 1.00 A C
+ATOM 20 CA THR A 20 29.459 23.465 1.648 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_6.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_6.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_6.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.295 12.856 -5.265 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.392 15.654 -3.421 1.00 1.00 A C
+ATOM 3 CA ILE A 3 23.452 16.562 0.099 1.00 1.00 A C
+ATOM 4 CA GLN A 4 21.517 18.878 2.265 1.00 1.00 A C
+ATOM 5 CA ASN A 5 22.809 21.068 5.176 1.00 1.00 A C
+ATOM 6 CA GLY A 6 20.450 23.452 7.208 1.00 1.00 A C
+ATOM 7 CA SER A 7 18.559 24.798 4.172 1.00 1.00 A C
+ATOM 8 CA THR A 8 20.909 24.370 1.224 1.00 1.00 A C
+ATOM 9 CA LYS A 9 20.572 21.559 -1.095 1.00 1.00 A C
+ATOM 10 CA TRP A 10 23.657 20.909 -3.261 1.00 1.00 A C
+ATOM 11 CA TYR A 11 24.662 17.909 -5.582 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.152 16.811 -5.103 1.00 1.00 A C
+ATOM 13 CA ASN A 13 29.675 13.411 -5.899 1.00 1.00 A C
+ATOM 14 CA GLY A 14 32.999 11.817 -5.333 1.00 1.00 A C
+ATOM 15 CA SER A 15 34.631 14.632 -3.252 1.00 1.00 A C
+ATOM 16 CA THR A 16 32.267 14.243 -0.281 1.00 1.00 A C
+ATOM 17 CA LYS A 17 33.952 15.213 2.849 1.00 1.00 A C
+ATOM 18 CA ILE A 18 32.455 15.355 6.296 1.00 1.00 A C
+ATOM 19 CA TYR A 19 29.750 18.082 6.415 1.00 1.00 A C
+ATOM 20 CA THR A 20 28.878 19.290 9.873 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_7.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_7.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_7.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.683 12.426 -4.729 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.407 15.043 -3.261 1.00 1.00 A C
+ATOM 3 CA ILE A 3 23.374 15.762 0.275 1.00 1.00 A C
+ATOM 4 CA GLN A 4 21.534 17.949 2.629 1.00 1.00 A C
+ATOM 5 CA ASN A 5 23.302 19.741 5.381 1.00 1.00 A C
+ATOM 6 CA GLY A 6 20.985 21.660 7.595 1.00 1.00 A C
+ATOM 7 CA SER A 7 18.526 22.931 4.881 1.00 1.00 A C
+ATOM 8 CA THR A 8 20.609 23.136 1.661 1.00 1.00 A C
+ATOM 9 CA LYS A 9 21.132 20.402 -0.997 1.00 1.00 A C
+ATOM 10 CA TRP A 10 24.426 20.330 -2.832 1.00 1.00 A C
+ATOM 11 CA TYR A 11 25.272 18.270 -5.977 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.346 16.497 -4.993 1.00 1.00 A C
+ATOM 13 CA ASN A 13 30.397 13.627 -6.488 1.00 1.00 A C
+ATOM 14 CA GLY A 14 32.365 10.905 -4.802 1.00 1.00 A C
+ATOM 15 CA SER A 15 33.678 12.367 -1.567 1.00 1.00 A C
+ATOM 16 CA THR A 16 30.964 13.580 0.651 1.00 1.00 A C
+ATOM 17 CA LYS A 17 32.099 16.817 2.236 1.00 1.00 A C
+ATOM 18 CA ILE A 18 30.689 17.558 5.677 1.00 1.00 A C
+ATOM 19 CA TYR A 19 31.031 21.351 6.250 1.00 1.00 A C
+ATOM 20 CA THR A 20 30.595 20.819 10.004 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_8.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_8.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_8.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 22.519 13.738 -5.798 1.00 1.00 A C
+ATOM 2 CA TRP A 2 21.680 17.063 -4.195 1.00 1.00 A C
+ATOM 3 CA ILE A 3 20.960 15.862 -0.633 1.00 1.00 A C
+ATOM 4 CA GLN A 4 19.643 18.019 2.060 1.00 1.00 A C
+ATOM 5 CA ASN A 5 22.550 18.355 4.583 1.00 1.00 A C
+ATOM 6 CA GLY A 6 22.112 20.686 7.505 1.00 1.00 A C
+ATOM 7 CA SER A 7 19.647 23.169 6.024 1.00 1.00 A C
+ATOM 8 CA THR A 8 20.956 23.241 2.486 1.00 1.00 A C
+ATOM 9 CA LYS A 9 20.937 21.208 -0.809 1.00 1.00 A C
+ATOM 10 CA TRP A 10 24.400 19.717 -1.105 1.00 1.00 A C
+ATOM 11 CA TYR A 11 25.837 17.159 -3.476 1.00 1.00 A C
+ATOM 12 CA GLN A 12 27.076 13.646 -2.810 1.00 1.00 A C
+ATOM 13 CA ASN A 13 29.300 12.125 -5.376 1.00 1.00 A C
+ATOM 14 CA GLY A 14 31.284 9.550 -3.459 1.00 1.00 A C
+ATOM 15 CA SER A 15 33.886 11.627 -1.711 1.00 1.00 A C
+ATOM 16 CA THR A 16 34.420 13.346 1.619 1.00 1.00 A C
+ATOM 17 CA LYS A 17 33.324 16.930 1.528 1.00 1.00 A C
+ATOM 18 CA ILE A 18 33.972 19.666 3.964 1.00 1.00 A C
+ATOM 19 CA TYR A 19 30.350 20.843 3.722 1.00 1.00 A C
+ATOM 20 CA THR A 20 28.975 20.298 7.213 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_9.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_9.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_2_9.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.035 13.320 -4.882 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.354 16.633 -3.898 1.00 1.00 A C
+ATOM 3 CA ILE A 3 22.053 16.244 -0.186 1.00 1.00 A C
+ATOM 4 CA GLN A 4 19.755 18.312 1.908 1.00 1.00 A C
+ATOM 5 CA ASN A 5 22.029 19.088 4.784 1.00 1.00 A C
+ATOM 6 CA GLY A 6 19.350 20.889 6.990 1.00 1.00 A C
+ATOM 7 CA SER A 7 18.274 23.699 4.669 1.00 1.00 A C
+ATOM 8 CA THR A 8 21.392 23.683 2.420 1.00 1.00 A C
+ATOM 9 CA LYS A 9 21.388 21.988 -0.938 1.00 1.00 A C
+ATOM 10 CA TRP A 10 24.885 20.857 -1.728 1.00 1.00 A C
+ATOM 11 CA TYR A 11 26.404 18.311 -4.108 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.370 15.289 -2.981 1.00 1.00 A C
+ATOM 13 CA ASN A 13 30.730 13.627 -5.396 1.00 1.00 A C
+ATOM 14 CA GLY A 14 29.909 10.201 -4.129 1.00 1.00 A C
+ATOM 15 CA SER A 15 31.606 9.694 -0.709 1.00 1.00 A C
+ATOM 16 CA THR A 16 33.427 12.862 0.165 1.00 1.00 A C
+ATOM 17 CA LYS A 17 31.911 15.641 2.314 1.00 1.00 A C
+ATOM 18 CA ILE A 18 34.066 18.760 2.418 1.00 1.00 A C
+ATOM 19 CA TYR A 19 31.425 21.293 3.279 1.00 1.00 A C
+ATOM 20 CA THR A 20 30.831 20.349 7.034 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_3.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_3.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_3.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.509 14.166 -4.920 1.00 1.00 A C
+ATOM 2 CA TRP A 2 23.078 17.478 -3.578 1.00 1.00 A C
+ATOM 3 CA ILE A 3 21.301 16.616 -0.282 1.00 1.00 A C
+ATOM 4 CA GLN A 4 19.076 19.523 0.855 1.00 1.00 A C
+ATOM 5 CA ASN A 5 17.626 19.836 4.335 1.00 1.00 A C
+ATOM 6 CA GLY A 6 15.313 22.718 4.099 1.00 1.00 A C
+ATOM 7 CA SER A 7 18.087 25.363 3.755 1.00 1.00 A C
+ATOM 8 CA THR A 8 21.252 23.410 4.694 1.00 1.00 A C
+ATOM 9 CA LYS A 9 23.113 21.649 1.888 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.888 19.200 1.199 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.444 17.516 -1.902 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.305 13.984 -1.196 1.00 1.00 A C
+ATOM 13 CA ASN A 13 31.434 13.220 -2.888 1.00 1.00 A C
+ATOM 14 CA GLY A 14 33.190 9.944 -2.608 1.00 1.00 A C
+ATOM 15 CA SER A 15 32.328 9.473 1.051 1.00 1.00 A C
+ATOM 16 CA THR A 16 33.877 11.973 3.551 1.00 1.00 A C
+ATOM 17 CA LYS A 17 34.292 14.764 0.954 1.00 1.00 A C
+ATOM 18 CA ILE A 18 31.507 17.086 1.720 1.00 1.00 A C
+ATOM 19 CA TYR A 19 31.041 20.138 -0.512 1.00 1.00 A C
+ATOM 20 CA THR A 20 28.639 23.120 -0.025 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_30.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_30.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_30.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.242 15.123 -6.583 1.00 1.00 A C
+ATOM 2 CA TRP A 2 23.126 17.647 -4.049 1.00 1.00 A C
+ATOM 3 CA ILE A 3 21.682 16.066 -0.906 1.00 1.00 A C
+ATOM 4 CA GLN A 4 20.084 18.106 1.915 1.00 1.00 A C
+ATOM 5 CA ASN A 5 21.516 17.264 5.428 1.00 1.00 A C
+ATOM 6 CA GLY A 6 20.933 19.637 8.231 1.00 1.00 A C
+ATOM 7 CA SER A 7 20.613 23.146 6.613 1.00 1.00 A C
+ATOM 8 CA THR A 8 21.517 23.346 2.854 1.00 1.00 A C
+ATOM 9 CA LYS A 9 22.391 20.888 0.071 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.787 19.528 0.173 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.392 17.861 -2.782 1.00 1.00 A C
+ATOM 12 CA GLN A 12 27.936 14.222 -2.463 1.00 1.00 A C
+ATOM 13 CA ASN A 13 31.341 13.404 -3.936 1.00 1.00 A C
+ATOM 14 CA GLY A 14 31.308 9.709 -3.109 1.00 1.00 A C
+ATOM 15 CA SER A 15 32.163 9.761 0.667 1.00 1.00 A C
+ATOM 16 CA THR A 16 32.888 13.419 1.328 1.00 1.00 A C
+ATOM 17 CA LYS A 17 30.233 16.085 1.266 1.00 1.00 A C
+ATOM 18 CA ILE A 18 31.446 18.988 -0.629 1.00 1.00 A C
+ATOM 19 CA TYR A 19 29.934 21.799 1.390 1.00 1.00 A C
+ATOM 20 CA THR A 20 28.276 24.393 -1.043 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_31.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_31.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_31.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.970 13.268 -5.417 1.00 1.00 A C
+ATOM 2 CA TRP A 2 23.288 16.402 -4.056 1.00 1.00 A C
+ATOM 3 CA ILE A 3 21.657 15.735 -0.612 1.00 1.00 A C
+ATOM 4 CA GLN A 4 19.362 18.487 0.537 1.00 1.00 A C
+ATOM 5 CA ASN A 5 19.144 18.356 4.364 1.00 1.00 A C
+ATOM 6 CA GLY A 6 17.210 21.531 4.872 1.00 1.00 A C
+ATOM 7 CA SER A 7 19.783 24.421 4.998 1.00 1.00 A C
+ATOM 8 CA THR A 8 22.769 22.072 5.026 1.00 1.00 A C
+ATOM 9 CA LYS A 9 23.243 21.634 1.271 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.808 18.848 0.383 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.359 17.883 -2.804 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.609 14.455 -1.949 1.00 1.00 A C
+ATOM 13 CA ASN A 13 31.043 13.342 -4.609 1.00 1.00 A C
+ATOM 14 CA GLY A 14 31.123 9.761 -3.209 1.00 1.00 A C
+ATOM 15 CA SER A 15 32.993 10.346 -0.004 1.00 1.00 A C
+ATOM 16 CA THR A 16 33.964 14.041 -0.444 1.00 1.00 A C
+ATOM 17 CA LYS A 17 31.355 16.403 1.001 1.00 1.00 A C
+ATOM 18 CA ILE A 18 31.209 19.890 -0.638 1.00 1.00 A C
+ATOM 19 CA TYR A 19 29.567 22.455 1.634 1.00 1.00 A C
+ATOM 20 CA THR A 20 27.508 24.566 -0.592 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_4.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_4.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_4.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 25.693 13.770 -4.875 1.00 1.00 A C
+ATOM 2 CA TRP A 2 23.228 16.580 -4.231 1.00 1.00 A C
+ATOM 3 CA ILE A 3 22.236 16.463 -0.650 1.00 1.00 A C
+ATOM 4 CA GLN A 4 19.794 18.333 1.448 1.00 1.00 A C
+ATOM 5 CA ASN A 5 19.049 18.009 5.136 1.00 1.00 A C
+ATOM 6 CA GLY A 6 16.419 20.659 6.079 1.00 1.00 A C
+ATOM 7 CA SER A 7 16.240 23.900 4.201 1.00 1.00 A C
+ATOM 8 CA THR A 8 19.828 24.062 3.008 1.00 1.00 A C
+ATOM 9 CA LYS A 9 21.369 22.723 -0.153 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.028 21.733 -0.048 1.00 1.00 A C
+ATOM 11 CA TYR A 11 27.079 19.324 -2.216 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.731 15.977 -1.474 1.00 1.00 A C
+ATOM 13 CA ASN A 13 31.767 14.428 -3.209 1.00 1.00 A C
+ATOM 14 CA GLY A 14 30.007 11.198 -3.651 1.00 1.00 A C
+ATOM 15 CA SER A 15 29.241 9.859 -0.240 1.00 1.00 A C
+ATOM 16 CA THR A 16 32.514 11.279 1.300 1.00 1.00 A C
+ATOM 17 CA LYS A 17 33.671 14.853 1.409 1.00 1.00 A C
+ATOM 18 CA ILE A 18 31.276 17.586 2.246 1.00 1.00 A C
+ATOM 19 CA TYR A 19 31.304 20.869 0.273 1.00 1.00 A C
+ATOM 20 CA THR A 20 29.466 23.386 2.612 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_5.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_5.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_5.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.354 13.682 -3.743 1.00 1.00 A C
+ATOM 2 CA TRP A 2 23.172 17.338 -4.179 1.00 1.00 A C
+ATOM 3 CA ILE A 3 21.997 16.774 -0.851 1.00 1.00 A C
+ATOM 4 CA GLN A 4 19.412 18.905 0.748 1.00 1.00 A C
+ATOM 5 CA ASN A 5 19.214 18.564 4.550 1.00 1.00 A C
+ATOM 6 CA GLY A 6 15.997 20.100 5.704 1.00 1.00 A C
+ATOM 7 CA SER A 7 16.517 23.713 4.908 1.00 1.00 A C
+ATOM 8 CA THR A 8 20.118 23.883 3.679 1.00 1.00 A C
+ATOM 9 CA LYS A 9 21.506 22.283 0.476 1.00 1.00 A C
+ATOM 10 CA TRP A 10 25.006 21.015 -0.140 1.00 1.00 A C
+ATOM 11 CA TYR A 11 26.847 18.360 -2.163 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.389 14.919 -1.138 1.00 1.00 A C
+ATOM 13 CA ASN A 13 31.130 13.502 -3.394 1.00 1.00 A C
+ATOM 14 CA GLY A 14 32.022 9.924 -2.756 1.00 1.00 A C
+ATOM 15 CA SER A 15 31.032 9.386 0.897 1.00 1.00 A C
+ATOM 16 CA THR A 16 33.762 11.643 2.218 1.00 1.00 A C
+ATOM 17 CA LYS A 17 33.747 15.072 0.560 1.00 1.00 A C
+ATOM 18 CA ILE A 18 31.016 17.265 2.143 1.00 1.00 A C
+ATOM 19 CA TYR A 19 31.076 20.325 -0.073 1.00 1.00 A C
+ATOM 20 CA THR A 20 29.459 23.465 1.648 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_6.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_6.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_6.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.295 12.856 -5.265 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.392 15.654 -3.421 1.00 1.00 A C
+ATOM 3 CA ILE A 3 23.452 16.562 0.099 1.00 1.00 A C
+ATOM 4 CA GLN A 4 21.517 18.878 2.265 1.00 1.00 A C
+ATOM 5 CA ASN A 5 22.809 21.068 5.176 1.00 1.00 A C
+ATOM 6 CA GLY A 6 20.450 23.452 7.208 1.00 1.00 A C
+ATOM 7 CA SER A 7 18.559 24.798 4.172 1.00 1.00 A C
+ATOM 8 CA THR A 8 20.909 24.370 1.224 1.00 1.00 A C
+ATOM 9 CA LYS A 9 20.572 21.559 -1.095 1.00 1.00 A C
+ATOM 10 CA TRP A 10 23.657 20.909 -3.261 1.00 1.00 A C
+ATOM 11 CA TYR A 11 24.662 17.909 -5.582 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.152 16.811 -5.103 1.00 1.00 A C
+ATOM 13 CA ASN A 13 29.675 13.411 -5.899 1.00 1.00 A C
+ATOM 14 CA GLY A 14 32.999 11.817 -5.333 1.00 1.00 A C
+ATOM 15 CA SER A 15 34.631 14.632 -3.252 1.00 1.00 A C
+ATOM 16 CA THR A 16 32.267 14.243 -0.281 1.00 1.00 A C
+ATOM 17 CA LYS A 17 33.952 15.213 2.849 1.00 1.00 A C
+ATOM 18 CA ILE A 18 32.455 15.355 6.296 1.00 1.00 A C
+ATOM 19 CA TYR A 19 29.750 18.082 6.415 1.00 1.00 A C
+ATOM 20 CA THR A 20 28.878 19.290 9.873 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_7.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_7.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_7.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.683 12.426 -4.729 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.407 15.043 -3.261 1.00 1.00 A C
+ATOM 3 CA ILE A 3 23.374 15.762 0.275 1.00 1.00 A C
+ATOM 4 CA GLN A 4 21.534 17.949 2.629 1.00 1.00 A C
+ATOM 5 CA ASN A 5 23.302 19.741 5.381 1.00 1.00 A C
+ATOM 6 CA GLY A 6 20.985 21.660 7.595 1.00 1.00 A C
+ATOM 7 CA SER A 7 18.526 22.931 4.881 1.00 1.00 A C
+ATOM 8 CA THR A 8 20.609 23.136 1.661 1.00 1.00 A C
+ATOM 9 CA LYS A 9 21.132 20.402 -0.997 1.00 1.00 A C
+ATOM 10 CA TRP A 10 24.426 20.330 -2.832 1.00 1.00 A C
+ATOM 11 CA TYR A 11 25.272 18.270 -5.977 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.346 16.497 -4.993 1.00 1.00 A C
+ATOM 13 CA ASN A 13 30.397 13.627 -6.488 1.00 1.00 A C
+ATOM 14 CA GLY A 14 32.365 10.905 -4.802 1.00 1.00 A C
+ATOM 15 CA SER A 15 33.678 12.367 -1.567 1.00 1.00 A C
+ATOM 16 CA THR A 16 30.964 13.580 0.651 1.00 1.00 A C
+ATOM 17 CA LYS A 17 32.099 16.817 2.236 1.00 1.00 A C
+ATOM 18 CA ILE A 18 30.689 17.558 5.677 1.00 1.00 A C
+ATOM 19 CA TYR A 19 31.031 21.351 6.250 1.00 1.00 A C
+ATOM 20 CA THR A 20 30.595 20.819 10.004 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_8.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_8.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_8.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 22.519 13.738 -5.798 1.00 1.00 A C
+ATOM 2 CA TRP A 2 21.680 17.063 -4.195 1.00 1.00 A C
+ATOM 3 CA ILE A 3 20.960 15.862 -0.633 1.00 1.00 A C
+ATOM 4 CA GLN A 4 19.643 18.019 2.060 1.00 1.00 A C
+ATOM 5 CA ASN A 5 22.550 18.355 4.583 1.00 1.00 A C
+ATOM 6 CA GLY A 6 22.112 20.686 7.505 1.00 1.00 A C
+ATOM 7 CA SER A 7 19.647 23.169 6.024 1.00 1.00 A C
+ATOM 8 CA THR A 8 20.956 23.241 2.486 1.00 1.00 A C
+ATOM 9 CA LYS A 9 20.937 21.208 -0.809 1.00 1.00 A C
+ATOM 10 CA TRP A 10 24.400 19.717 -1.105 1.00 1.00 A C
+ATOM 11 CA TYR A 11 25.837 17.159 -3.476 1.00 1.00 A C
+ATOM 12 CA GLN A 12 27.076 13.646 -2.810 1.00 1.00 A C
+ATOM 13 CA ASN A 13 29.300 12.125 -5.376 1.00 1.00 A C
+ATOM 14 CA GLY A 14 31.284 9.550 -3.459 1.00 1.00 A C
+ATOM 15 CA SER A 15 33.886 11.627 -1.711 1.00 1.00 A C
+ATOM 16 CA THR A 16 34.420 13.346 1.619 1.00 1.00 A C
+ATOM 17 CA LYS A 17 33.324 16.930 1.528 1.00 1.00 A C
+ATOM 18 CA ILE A 18 33.972 19.666 3.964 1.00 1.00 A C
+ATOM 19 CA TYR A 19 30.350 20.843 3.722 1.00 1.00 A C
+ATOM 20 CA THR A 20 28.975 20.298 7.213 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_9.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_9.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/initial_config_c_alpha_9.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+ATOM 1 CA THR A 1 24.035 13.320 -4.882 1.00 1.00 A C
+ATOM 2 CA TRP A 2 22.354 16.633 -3.898 1.00 1.00 A C
+ATOM 3 CA ILE A 3 22.053 16.244 -0.186 1.00 1.00 A C
+ATOM 4 CA GLN A 4 19.755 18.312 1.908 1.00 1.00 A C
+ATOM 5 CA ASN A 5 22.029 19.088 4.784 1.00 1.00 A C
+ATOM 6 CA GLY A 6 19.350 20.889 6.990 1.00 1.00 A C
+ATOM 7 CA SER A 7 18.274 23.699 4.669 1.00 1.00 A C
+ATOM 8 CA THR A 8 21.392 23.683 2.420 1.00 1.00 A C
+ATOM 9 CA LYS A 9 21.388 21.988 -0.938 1.00 1.00 A C
+ATOM 10 CA TRP A 10 24.885 20.857 -1.728 1.00 1.00 A C
+ATOM 11 CA TYR A 11 26.404 18.311 -4.108 1.00 1.00 A C
+ATOM 12 CA GLN A 12 28.370 15.289 -2.981 1.00 1.00 A C
+ATOM 13 CA ASN A 13 30.730 13.627 -5.396 1.00 1.00 A C
+ATOM 14 CA GLY A 14 29.909 10.201 -4.129 1.00 1.00 A C
+ATOM 15 CA SER A 15 31.606 9.694 -0.709 1.00 1.00 A C
+ATOM 16 CA THR A 16 33.427 12.862 0.165 1.00 1.00 A C
+ATOM 17 CA LYS A 17 31.911 15.641 2.314 1.00 1.00 A C
+ATOM 18 CA ILE A 18 34.066 18.760 2.418 1.00 1.00 A C
+ATOM 19 CA TYR A 19 31.425 21.293 3.279 1.00 1.00 A C
+ATOM 20 CA THR A 20 30.831 20.349 7.034 1.00 1.00 A C
Added: SwiftApps/CMTS/stringmethod/src/data/repulsive-potential-energy
===================================================================
Added: SwiftApps/CMTS/stringmethod/src/data/rmsd_from_structure_1_with_time
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/rmsd_from_structure_1_with_time (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/rmsd_from_structure_1_with_time 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,32 @@
+0 0.00000000e+00 1.685674909694776e+00
+1 0.00000000e+00 2.171061806239006e+00
+2 0.00000000e+00 1.704441783037848e+00
+3 0.00000000e+00 1.599452106222534e+00
+4 0.00000000e+00 1.896360901907732e+00
+5 0.00000000e+00 1.673162534664162e+00
+6 0.00000000e+00 2.993249724847024e+00
+7 0.00000000e+00 2.936699147867777e+00
+8 0.00000000e+00 2.449900742753989e+00
+9 0.00000000e+00 1.993527944062859e+00
+10 0.00000000e+00 1.162160065908141e+00
+11 0.00000000e+00 1.348989962435402e+00
+12 0.00000000e+00 1.561534793108840e+00
+13 0.00000000e+00 1.543622861124544e+00
+14 0.00000000e+00 1.485168293991412e+00
+15 0.00000000e+00 1.534011862097476e+00
+16 0.00000000e+00 1.242636449575892e+00
+17 0.00000000e+00 1.395321815258305e+00
+18 0.00000000e+00 1.005920154626937e+00
+19 0.00000000e+00 1.024215412867905e+00
+20 0.00000000e+00 9.626248154831045e-01
+21 0.00000000e+00 9.198497273238577e-01
+22 0.00000000e+00 1.159603622028816e+00
+23 0.00000000e+00 8.463803115536406e-01
+24 0.00000000e+00 8.828584743899467e-01
+25 0.00000000e+00 1.293246868619585e+00
+26 0.00000000e+00 1.125471359772386e+00
+27 0.00000000e+00 1.419359662900580e+00
+28 0.00000000e+00 1.189508949837841e+00
+29 0.00000000e+00 1.807091321137425e+00
+30 0.00000000e+00 1.627056829118097e+00
+31 0.00000000e+00 8.790906586891225e-01
Added: SwiftApps/CMTS/stringmethod/src/data/rmsd_from_structure_1b_with_time
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/rmsd_from_structure_1b_with_time (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/rmsd_from_structure_1b_with_time 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,32 @@
+0 0.00000000e+00 1.415875956309667e+00
+1 0.00000000e+00 1.842864311548616e+00
+2 0.00000000e+00 1.445935620082528e+00
+3 0.00000000e+00 1.431693349358403e+00
+4 0.00000000e+00 1.664724406500748e+00
+5 0.00000000e+00 1.460339294114553e+00
+6 0.00000000e+00 2.615152113147483e+00
+7 0.00000000e+00 2.670046933797320e+00
+8 0.00000000e+00 2.140264051456285e+00
+9 0.00000000e+00 1.808357392732853e+00
+10 0.00000000e+00 7.719801783507165e-01
+11 0.00000000e+00 1.029486265877261e+00
+12 0.00000000e+00 1.307088283713317e+00
+13 0.00000000e+00 1.181301439485999e+00
+14 0.00000000e+00 1.221422144073387e+00
+15 0.00000000e+00 1.310819941864147e+00
+16 0.00000000e+00 9.928649461129012e-01
+17 0.00000000e+00 1.109158912673940e+00
+18 0.00000000e+00 8.012471529781072e-01
+19 0.00000000e+00 7.526971187148471e-01
+20 0.00000000e+00 8.260809829798597e-01
+21 0.00000000e+00 7.245994896226874e-01
+22 0.00000000e+00 8.676376869662700e-01
+23 0.00000000e+00 6.407409382231349e-01
+24 0.00000000e+00 7.354954210862731e-01
+25 0.00000000e+00 1.053829306420485e+00
+26 0.00000000e+00 9.250940032917452e-01
+27 0.00000000e+00 1.130501830654493e+00
+28 0.00000000e+00 9.689114925673895e-01
+29 0.00000000e+00 1.628079417523752e+00
+30 0.00000000e+00 1.393015530982055e+00
+31 0.00000000e+00 7.145042548443306e-01
Added: SwiftApps/CMTS/stringmethod/src/data/rmsd_from_structure_2_with_time
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/rmsd_from_structure_2_with_time (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/rmsd_from_structure_2_with_time 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,32 @@
+0 0.00000000e+00 8.086696048572092e-01
+1 0.00000000e+00 1.451931376614474e+00
+2 0.00000000e+00 2.725970482345005e+00
+3 0.00000000e+00 2.521256317824526e+00
+4 0.00000000e+00 2.642482970368894e+00
+5 0.00000000e+00 2.571278291915656e+00
+6 0.00000000e+00 2.806385107790291e+00
+7 0.00000000e+00 2.467247394651727e+00
+8 0.00000000e+00 2.461586198275849e+00
+9 0.00000000e+00 2.336944662722501e+00
+10 0.00000000e+00 1.989748680355332e+00
+11 0.00000000e+00 2.196328479782746e+00
+12 0.00000000e+00 2.482384883408453e+00
+13 0.00000000e+00 1.955894451653418e+00
+14 0.00000000e+00 2.186400757173653e+00
+15 0.00000000e+00 2.123106598808847e+00
+16 0.00000000e+00 1.811926950955804e+00
+17 0.00000000e+00 2.012722961630359e+00
+18 0.00000000e+00 2.037946001882286e+00
+19 0.00000000e+00 1.941387385011458e+00
+20 0.00000000e+00 1.910015010565207e+00
+21 0.00000000e+00 1.725648446575387e+00
+22 0.00000000e+00 1.942518952429652e+00
+23 0.00000000e+00 1.670391799174977e+00
+24 0.00000000e+00 1.811531871812339e+00
+25 0.00000000e+00 1.744813982865583e+00
+26 0.00000000e+00 1.785652683696837e+00
+27 0.00000000e+00 1.939394919210865e+00
+28 0.00000000e+00 1.749017260836265e+00
+29 0.00000000e+00 1.897882053089679e+00
+30 0.00000000e+00 1.874574505408660e+00
+31 0.00000000e+00 1.661317925429506e+00
Added: SwiftApps/CMTS/stringmethod/src/data/rmsd_from_structure_2b_with_time
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/rmsd_from_structure_2b_with_time (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/rmsd_from_structure_2b_with_time 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,32 @@
+0 0.00000000e+00 7.048985185484758e-01
+1 0.00000000e+00 1.246052282648948e+00
+2 0.00000000e+00 2.492208797847174e+00
+3 0.00000000e+00 2.367361661030586e+00
+4 0.00000000e+00 2.417422075246997e+00
+5 0.00000000e+00 2.405389076683745e+00
+6 0.00000000e+00 2.577886443773926e+00
+7 0.00000000e+00 2.269917572118093e+00
+8 0.00000000e+00 2.304366585153299e+00
+9 0.00000000e+00 2.103079289916043e+00
+10 0.00000000e+00 1.680180193069180e+00
+11 0.00000000e+00 1.955244974382588e+00
+12 0.00000000e+00 2.284968500132767e+00
+13 0.00000000e+00 1.744052638724799e+00
+14 0.00000000e+00 1.960540030930555e+00
+15 0.00000000e+00 1.903050212537033e+00
+16 0.00000000e+00 1.495031257620251e+00
+17 0.00000000e+00 1.672723056674907e+00
+18 0.00000000e+00 1.687909909067618e+00
+19 0.00000000e+00 1.546117463106460e+00
+20 0.00000000e+00 1.556908666159033e+00
+21 0.00000000e+00 1.295906704218784e+00
+22 0.00000000e+00 1.569467664920430e+00
+23 0.00000000e+00 1.309650560007883e+00
+24 0.00000000e+00 1.459299776621707e+00
+25 0.00000000e+00 1.387253780996019e+00
+26 0.00000000e+00 1.432023920224694e+00
+27 0.00000000e+00 1.527901538067398e+00
+28 0.00000000e+00 1.356366323973027e+00
+29 0.00000000e+00 1.676852396783044e+00
+30 0.00000000e+00 1.567827170393039e+00
+31 0.00000000e+00 1.256644769074214e+00
Added: SwiftApps/CMTS/stringmethod/src/data/track-progress
===================================================================
Added: SwiftApps/CMTS/stringmethod/src/data/trajectory_all_0.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/trajectory_all_0.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/trajectory_all_0.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,40 @@
+MODEL 0
+ATOM 1 CA THR A 1 24.673 12.849 -5.563 1.00 1.00 A C
+ATOM 2 CB THR A 2 23.807 11.647 -5.280 1.00 1.00 A C
+ATOM 3 CA TRP A 3 23.214 16.010 -3.963 1.00 1.00 A C
+ATOM 4 CB TRP A 4 22.750 17.253 -4.695 1.00 1.00 A C
+ATOM 5 CA ILE A 5 21.548 16.254 -0.576 1.00 1.00 A C
+ATOM 6 CB ILE A 6 21.881 15.350 0.644 1.00 1.00 A C
+ATOM 7 CA GLN A 7 20.016 19.808 -0.155 1.00 1.00 A C
+ATOM 8 CB GLN A 8 19.036 20.640 -1.095 1.00 1.00 A C
+ATOM 9 CA ASN A 9 19.099 20.043 3.540 1.00 1.00 A C
+ATOM 10 CB ASN A 10 19.291 18.912 4.592 1.00 1.00 A C
+ATOM 11 CA GLY A 11 18.524 23.803 3.815 1.00 1.00 A C
+ATOM 12 CA SER A 12 21.444 25.372 5.538 1.00 1.00 A C
+ATOM 13 CB SER A 13 21.565 25.731 7.024 1.00 1.00 A C
+ATOM 14 CA THR A 14 24.070 22.640 4.658 1.00 1.00 A C
+ATOM 15 CB THR A 15 24.767 22.084 5.936 1.00 1.00 A C
+ATOM 16 CA LYS A 16 24.134 20.811 1.513 1.00 1.00 A C
+ATOM 17 CB LYS A 17 23.904 21.618 0.361 1.00 1.00 A C
+ATOM 18 CA TRP A 18 25.793 17.385 1.534 1.00 1.00 A C
+ATOM 19 CB TRP A 19 25.332 16.230 2.469 1.00 1.00 A C
+ATOM 20 CA TYR A 20 27.436 15.607 -1.401 1.00 1.00 A C
+ATOM 21 CB TYR A 21 28.213 16.700 -2.155 1.00 1.00 A C
+ATOM 22 CA GLN A 22 27.949 11.896 -1.672 1.00 1.00 A C
+ATOM 23 CB GLN A 23 26.847 10.837 -1.433 1.00 1.00 A C
+ATOM 24 CA ASN A 24 30.575 11.904 -4.260 1.00 1.00 A C
+ATOM 25 CB ASN A 25 30.856 13.286 -4.910 1.00 1.00 A C
+ATOM 26 CA GLY A 26 32.990 9.317 -2.740 1.00 1.00 A C
+ATOM 27 CA SER A 27 34.181 10.934 0.395 1.00 1.00 A C
+ATOM 28 CB SER A 28 35.574 11.210 0.810 1.00 1.00 A C
+ATOM 29 CA THR A 29 31.643 13.473 1.511 1.00 1.00 A C
+ATOM 30 CB THR A 30 30.786 13.264 2.744 1.00 1.00 A C
+ATOM 31 CA LYS A 31 31.955 17.104 0.909 1.00 1.00 A C
+ATOM 32 CB LYS A 32 32.300 17.434 -0.607 1.00 1.00 A C
+ATOM 33 CA ILE A 33 30.593 20.181 2.548 1.00 1.00 A C
+ATOM 34 CB ILE A 34 31.225 20.473 3.900 1.00 1.00 A C
+ATOM 35 CA TYR A 35 28.636 22.877 0.832 1.00 1.00 A C
+ATOM 36 CB TYR A 36 28.342 22.763 -0.670 1.00 1.00 A C
+ATOM 37 CA THR A 37 26.003 25.623 1.670 1.00 1.00 A C
+ATOM 38 CB THR A 38 26.472 26.937 2.335 1.00 1.00 A C
+ENDMDL
Added: SwiftApps/CMTS/stringmethod/src/data/trajectory_all_1.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/trajectory_all_1.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/trajectory_all_1.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,40 @@
+MODEL 0
+ATOM 1 CA THR A 1 23.546 11.933 -4.152 1.00 1.00 A C
+ATOM 2 CB THR A 2 24.169 10.761 -3.383 1.00 1.00 A C
+ATOM 3 CA TRP A 3 23.092 15.533 -3.095 1.00 1.00 A C
+ATOM 4 CB TRP A 4 22.647 16.450 -4.168 1.00 1.00 A C
+ATOM 5 CA ILE A 5 21.586 16.045 0.423 1.00 1.00 A C
+ATOM 6 CB ILE A 6 22.093 15.625 1.813 1.00 1.00 A C
+ATOM 7 CA GLN A 7 19.383 19.118 -0.271 1.00 1.00 A C
+ATOM 8 CB GLN A 8 18.456 19.340 -1.496 1.00 1.00 A C
+ATOM 9 CA ASN A 9 18.924 20.615 3.129 1.00 1.00 A C
+ATOM 10 CB ASN A 10 19.758 20.058 4.323 1.00 1.00 A C
+ATOM 11 CA GLY A 11 17.682 24.082 2.309 1.00 1.00 A C
+ATOM 12 CA SER A 12 20.285 25.605 0.166 1.00 1.00 A C
+ATOM 13 CB SER A 13 20.497 27.043 0.573 1.00 1.00 A C
+ATOM 14 CA THR A 14 23.149 23.575 1.748 1.00 1.00 A C
+ATOM 15 CB THR A 15 23.744 23.787 3.126 1.00 1.00 A C
+ATOM 16 CA LYS A 16 23.540 20.884 -0.781 1.00 1.00 A C
+ATOM 17 CB LYS A 17 23.616 21.147 -2.317 1.00 1.00 A C
+ATOM 18 CA TRP A 18 25.473 18.167 1.163 1.00 1.00 A C
+ATOM 19 CB TRP A 19 25.105 17.682 2.497 1.00 1.00 A C
+ATOM 20 CA TYR A 20 27.403 16.255 -1.719 1.00 1.00 A C
+ATOM 21 CB TYR A 21 28.197 17.102 -2.716 1.00 1.00 A C
+ATOM 22 CA GLN A 22 28.017 12.473 -1.486 1.00 1.00 A C
+ATOM 23 CB GLN A 23 26.868 11.512 -1.007 1.00 1.00 A C
+ATOM 24 CA ASN A 24 29.157 11.132 -4.922 1.00 1.00 A C
+ATOM 25 CB ASN A 25 28.324 11.445 -6.145 1.00 1.00 A C
+ATOM 26 CA GLY A 26 33.003 11.091 -5.274 1.00 1.00 A C
+ATOM 27 CA SER A 27 33.863 13.286 -2.370 1.00 1.00 A C
+ATOM 28 CB SER A 28 34.783 14.463 -2.654 1.00 1.00 A C
+ATOM 29 CA THR A 29 31.872 13.825 0.775 1.00 1.00 A C
+ATOM 30 CB THR A 30 31.887 12.910 1.984 1.00 1.00 A C
+ATOM 31 CA LYS A 31 31.403 17.638 1.008 1.00 1.00 A C
+ATOM 32 CB LYS A 32 31.209 18.368 -0.332 1.00 1.00 A C
+ATOM 33 CA ILE A 33 30.057 18.320 4.446 1.00 1.00 A C
+ATOM 34 CB ILE A 34 30.108 17.390 5.592 1.00 1.00 A C
+ATOM 35 CA TYR A 35 29.835 22.075 4.711 1.00 1.00 A C
+ATOM 36 CB TYR A 36 28.720 22.821 3.921 1.00 1.00 A C
+ATOM 37 CA THR A 37 30.651 23.250 8.229 1.00 1.00 A C
+ATOM 38 CB THR A 38 32.058 22.986 8.887 1.00 1.00 A C
+ENDMDL
Added: SwiftApps/CMTS/stringmethod/src/data/trajectory_all_10.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/trajectory_all_10.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/trajectory_all_10.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,40 @@
+MODEL 0
+ATOM 1 CA THR A 1 24.419 12.685 -3.263 1.00 1.00 A C
+ATOM 2 CB THR A 2 24.942 11.940 -2.100 1.00 1.00 A C
+ATOM 3 CA TRP A 3 22.276 15.712 -2.827 1.00 1.00 A C
+ATOM 4 CB TRP A 4 21.207 16.074 -3.879 1.00 1.00 A C
+ATOM 5 CA ILE A 5 21.226 16.432 0.503 1.00 1.00 A C
+ATOM 6 CB ILE A 6 22.178 16.048 1.675 1.00 1.00 A C
+ATOM 7 CA GLN A 7 18.950 19.482 1.186 1.00 1.00 A C
+ATOM 8 CB GLN A 8 17.455 19.473 0.596 1.00 1.00 A C
+ATOM 9 CA ASN A 9 19.978 20.507 4.684 1.00 1.00 A C
+ATOM 10 CB ASN A 10 21.288 19.975 5.277 1.00 1.00 A C
+ATOM 11 CA GLY A 11 17.949 23.676 4.912 1.00 1.00 A C
+ATOM 12 CA SER A 12 20.481 26.308 3.873 1.00 1.00 A C
+ATOM 13 CB SER A 13 20.892 27.458 4.767 1.00 1.00 A C
+ATOM 14 CA THR A 14 23.516 24.060 3.804 1.00 1.00 A C
+ATOM 15 CB THR A 15 24.181 23.451 5.089 1.00 1.00 A C
+ATOM 16 CA LYS A 16 23.314 22.350 0.393 1.00 1.00 A C
+ATOM 17 CB LYS A 17 23.206 23.364 -0.721 1.00 1.00 A C
+ATOM 18 CA TRP A 18 25.297 19.185 1.008 1.00 1.00 A C
+ATOM 19 CB TRP A 19 25.018 18.371 2.246 1.00 1.00 A C
+ATOM 20 CA TYR A 20 26.810 17.848 -2.156 1.00 1.00 A C
+ATOM 21 CB TYR A 21 27.209 18.713 -3.313 1.00 1.00 A C
+ATOM 22 CA GLN A 22 28.656 14.531 -1.801 1.00 1.00 A C
+ATOM 23 CB GLN A 23 28.048 13.524 -0.787 1.00 1.00 A C
+ATOM 24 CA ASN A 24 30.468 12.966 -4.798 1.00 1.00 A C
+ATOM 25 CB ASN A 25 31.906 13.272 -5.115 1.00 1.00 A C
+ATOM 26 CA GLY A 26 29.975 9.649 -3.202 1.00 1.00 A C
+ATOM 27 CA SER A 27 32.431 9.524 -0.294 1.00 1.00 A C
+ATOM 28 CB SER A 28 33.589 8.575 -0.455 1.00 1.00 A C
+ATOM 29 CA THR A 29 33.863 12.946 0.247 1.00 1.00 A C
+ATOM 30 CB THR A 30 35.190 13.488 -0.302 1.00 1.00 A C
+ATOM 31 CA LYS A 31 31.233 15.535 1.105 1.00 1.00 A C
+ATOM 32 CB LYS A 32 30.282 15.474 2.257 1.00 1.00 A C
+ATOM 33 CA ILE A 33 32.610 18.526 -0.756 1.00 1.00 A C
+ATOM 34 CB ILE A 34 32.970 18.330 -2.207 1.00 1.00 A C
+ATOM 35 CA TYR A 35 29.870 21.300 -0.394 1.00 1.00 A C
+ATOM 36 CB TYR A 36 28.669 21.473 -1.351 1.00 1.00 A C
+ATOM 37 CA THR A 37 29.756 21.993 3.370 1.00 1.00 A C
+ATOM 38 CB THR A 38 31.174 21.649 3.981 1.00 1.00 A C
+ENDMDL
Added: SwiftApps/CMTS/stringmethod/src/data/trajectory_all_11.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/trajectory_all_11.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/trajectory_all_11.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,40 @@
+MODEL 0
+ATOM 1 CA THR A 1 23.950 12.754 -2.687 1.00 1.00 A C
+ATOM 2 CB THR A 2 24.613 12.116 -1.452 1.00 1.00 A C
+ATOM 3 CA TRP A 3 22.225 16.096 -1.947 1.00 1.00 A C
+ATOM 4 CB TRP A 4 21.274 16.780 -2.869 1.00 1.00 A C
+ATOM 5 CA ILE A 5 21.865 16.333 1.807 1.00 1.00 A C
+ATOM 6 CB ILE A 6 22.998 15.933 2.749 1.00 1.00 A C
+ATOM 7 CA GLN A 7 19.133 18.680 2.451 1.00 1.00 A C
+ATOM 8 CB GLN A 8 17.679 18.432 2.044 1.00 1.00 A C
+ATOM 9 CA ASN A 9 19.492 21.524 5.006 1.00 1.00 A C
+ATOM 10 CB ASN A 10 20.843 21.393 5.784 1.00 1.00 A C
+ATOM 11 CA GLY A 11 17.493 24.579 3.882 1.00 1.00 A C
+ATOM 12 CA SER A 12 19.961 26.565 1.758 1.00 1.00 A C
+ATOM 13 CB SER A 13 20.639 27.943 2.138 1.00 1.00 A C
+ATOM 14 CA THR A 14 23.048 24.417 2.185 1.00 1.00 A C
+ATOM 15 CB THR A 15 24.007 24.604 3.413 1.00 1.00 A C
+ATOM 16 CA LYS A 16 22.580 21.150 0.360 1.00 1.00 A C
+ATOM 17 CB LYS A 17 21.773 20.818 -0.890 1.00 1.00 A C
+ATOM 18 CA TRP A 18 25.653 19.062 0.978 1.00 1.00 A C
+ATOM 19 CB TRP A 19 26.034 18.719 2.430 1.00 1.00 A C
+ATOM 20 CA TYR A 20 27.037 17.293 -2.028 1.00 1.00 A C
+ATOM 21 CB TYR A 21 27.406 18.142 -3.292 1.00 1.00 A C
+ATOM 22 CA GLN A 22 28.326 13.916 -1.140 1.00 1.00 A C
+ATOM 23 CB GLN A 23 27.830 12.965 -0.105 1.00 1.00 A C
+ATOM 24 CA ASN A 24 29.714 13.147 -4.590 1.00 1.00 A C
+ATOM 25 CB ASN A 25 30.308 14.337 -5.380 1.00 1.00 A C
+ATOM 26 CA GLY A 26 30.463 9.490 -4.662 1.00 1.00 A C
+ATOM 27 CA SER A 27 33.694 9.112 -2.701 1.00 1.00 A C
+ATOM 28 CB SER A 28 35.004 8.608 -3.299 1.00 1.00 A C
+ATOM 29 CA THR A 29 34.195 12.758 -1.628 1.00 1.00 A C
+ATOM 30 CB THR A 30 35.138 13.727 -2.490 1.00 1.00 A C
+ATOM 31 CA LYS A 31 32.016 15.521 -0.003 1.00 1.00 A C
+ATOM 32 CB LYS A 32 31.458 15.181 1.348 1.00 1.00 A C
+ATOM 33 CA ILE A 33 32.618 19.021 -1.280 1.00 1.00 A C
+ATOM 34 CB ILE A 34 32.564 19.500 -2.710 1.00 1.00 A C
+ATOM 35 CA TYR A 35 30.441 20.995 1.106 1.00 1.00 A C
+ATOM 36 CB TYR A 36 29.180 21.673 0.572 1.00 1.00 A C
+ATOM 37 CA THR A 37 30.925 19.995 4.714 1.00 1.00 A C
+ATOM 38 CB THR A 38 32.204 19.317 5.051 1.00 1.00 A C
+ENDMDL
Added: SwiftApps/CMTS/stringmethod/src/data/trajectory_all_12.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/trajectory_all_12.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/trajectory_all_12.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,40 @@
+MODEL 0
+ATOM 1 CA THR A 1 23.915 12.437 -2.833 1.00 1.00 A C
+ATOM 2 CB THR A 2 24.501 11.393 -1.784 1.00 1.00 A C
+ATOM 3 CA TRP A 3 22.386 15.820 -1.546 1.00 1.00 A C
+ATOM 4 CB TRP A 4 21.477 16.540 -2.523 1.00 1.00 A C
+ATOM 5 CA ILE A 5 22.086 16.261 2.277 1.00 1.00 A C
+ATOM 6 CB ILE A 6 23.308 15.889 3.266 1.00 1.00 A C
+ATOM 7 CA GLN A 7 19.380 18.674 3.159 1.00 1.00 A C
+ATOM 8 CB GLN A 8 17.893 18.616 2.963 1.00 1.00 A C
+ATOM 9 CA ASN A 9 19.855 20.660 6.389 1.00 1.00 A C
+ATOM 10 CB ASN A 10 21.119 20.331 7.121 1.00 1.00 A C
+ATOM 11 CA GLY A 11 18.264 23.986 7.049 1.00 1.00 A C
+ATOM 12 CA SER A 12 18.738 25.910 3.879 1.00 1.00 A C
+ATOM 13 CB SER A 13 19.060 27.383 4.097 1.00 1.00 A C
+ATOM 14 CA THR A 14 21.878 24.973 2.416 1.00 1.00 A C
+ATOM 15 CB THR A 15 23.055 25.873 2.883 1.00 1.00 A C
+ATOM 16 CA LYS A 16 22.116 21.370 0.839 1.00 1.00 A C
+ATOM 17 CB LYS A 17 21.231 20.952 -0.305 1.00 1.00 A C
+ATOM 18 CA TRP A 18 25.483 19.651 0.700 1.00 1.00 A C
+ATOM 19 CB TRP A 19 26.221 19.581 2.058 1.00 1.00 A C
+ATOM 20 CA TYR A 20 26.630 17.372 -2.150 1.00 1.00 A C
+ATOM 21 CB TYR A 21 26.626 17.884 -3.571 1.00 1.00 A C
+ATOM 22 CA GLN A 22 28.696 14.386 -1.495 1.00 1.00 A C
+ATOM 23 CB GLN A 23 28.443 13.698 -0.136 1.00 1.00 A C
+ATOM 24 CA ASN A 24 29.715 12.409 -4.568 1.00 1.00 A C
+ATOM 25 CB ASN A 25 30.340 13.280 -5.610 1.00 1.00 A C
+ATOM 26 CA GLY A 26 30.319 8.879 -3.239 1.00 1.00 A C
+ATOM 27 CA SER A 27 33.683 9.250 -1.576 1.00 1.00 A C
+ATOM 28 CB SER A 28 34.909 8.550 -2.172 1.00 1.00 A C
+ATOM 29 CA THR A 29 34.923 12.834 -1.655 1.00 1.00 A C
+ATOM 30 CB THR A 30 35.820 13.439 -2.741 1.00 1.00 A C
+ATOM 31 CA LYS A 31 32.838 15.615 -0.395 1.00 1.00 A C
+ATOM 32 CB LYS A 32 32.412 15.595 1.100 1.00 1.00 A C
+ATOM 33 CA ILE A 33 32.778 18.832 -2.439 1.00 1.00 A C
+ATOM 34 CB ILE A 34 32.541 18.843 -3.939 1.00 1.00 A C
+ATOM 35 CA TYR A 35 30.068 20.939 -0.775 1.00 1.00 A C
+ATOM 36 CB TYR A 36 28.568 20.825 -1.075 1.00 1.00 A C
+ATOM 37 CA THR A 37 31.498 21.332 2.723 1.00 1.00 A C
+ATOM 38 CB THR A 38 33.021 21.425 3.078 1.00 1.00 A C
+ENDMDL
Added: SwiftApps/CMTS/stringmethod/src/data/trajectory_all_13.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/trajectory_all_13.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/trajectory_all_13.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,40 @@
+MODEL 0
+ATOM 1 CA THR A 1 23.321 12.731 -3.752 1.00 1.00 A C
+ATOM 2 CB THR A 2 22.665 11.669 -2.814 1.00 1.00 A C
+ATOM 3 CA TRP A 3 22.189 16.128 -2.341 1.00 1.00 A C
+ATOM 4 CB TRP A 4 21.378 17.082 -3.136 1.00 1.00 A C
+ATOM 5 CA ILE A 5 21.974 15.695 1.572 1.00 1.00 A C
+ATOM 6 CB ILE A 6 22.999 14.750 2.264 1.00 1.00 A C
+ATOM 7 CA GLN A 7 20.358 18.509 3.401 1.00 1.00 A C
+ATOM 8 CB GLN A 8 18.878 18.880 3.256 1.00 1.00 A C
+ATOM 9 CA ASN A 9 21.674 20.134 6.631 1.00 1.00 A C
+ATOM 10 CB ASN A 10 23.072 20.260 6.853 1.00 1.00 A C
+ATOM 11 CA GLY A 11 18.559 22.348 6.596 1.00 1.00 A C
+ATOM 12 CA SER A 12 18.723 24.887 3.895 1.00 1.00 A C
+ATOM 13 CB SER A 13 18.706 26.404 4.170 1.00 1.00 A C
+ATOM 14 CA THR A 14 22.402 24.166 3.181 1.00 1.00 A C
+ATOM 15 CB THR A 15 23.418 24.908 3.964 1.00 1.00 A C
+ATOM 16 CA LYS A 16 22.194 21.105 1.138 1.00 1.00 A C
+ATOM 17 CB LYS A 17 21.132 21.145 -0.025 1.00 1.00 A C
+ATOM 18 CA TRP A 18 25.684 19.589 0.431 1.00 1.00 A C
+ATOM 19 CB TRP A 19 26.728 19.147 1.532 1.00 1.00 A C
+ATOM 20 CA TYR A 20 26.352 17.430 -2.546 1.00 1.00 A C
+ATOM 21 CB TYR A 21 26.439 17.886 -4.031 1.00 1.00 A C
+ATOM 22 CA GLN A 22 28.101 14.177 -1.938 1.00 1.00 A C
+ATOM 23 CB GLN A 23 27.446 13.047 -1.062 1.00 1.00 A C
+ATOM 24 CA ASN A 24 30.394 13.185 -4.838 1.00 1.00 A C
+ATOM 25 CB ASN A 25 31.454 14.219 -5.327 1.00 1.00 A C
+ATOM 26 CA GLY A 26 30.278 9.509 -3.970 1.00 1.00 A C
+ATOM 27 CA SER A 27 32.400 9.405 -0.743 1.00 1.00 A C
+ATOM 28 CB SER A 28 33.771 8.822 -0.722 1.00 1.00 A C
+ATOM 29 CA THR A 29 33.550 12.957 0.242 1.00 1.00 A C
+ATOM 30 CB THR A 30 34.934 13.328 -0.258 1.00 1.00 A C
+ATOM 31 CA LYS A 31 31.086 15.777 0.326 1.00 1.00 A C
+ATOM 32 CB LYS A 32 30.139 16.075 1.549 1.00 1.00 A C
+ATOM 33 CA ILE A 33 32.309 18.411 -1.981 1.00 1.00 A C
+ATOM 34 CB ILE A 34 32.299 18.538 -3.505 1.00 1.00 A C
+ATOM 35 CA TYR A 35 30.841 21.576 -0.642 1.00 1.00 A C
+ATOM 36 CB TYR A 36 29.381 22.031 -0.754 1.00 1.00 A C
+ATOM 37 CA THR A 37 32.252 23.275 2.592 1.00 1.00 A C
+ATOM 38 CB THR A 38 33.245 24.433 2.744 1.00 1.00 A C
+ENDMDL
Added: SwiftApps/CMTS/stringmethod/src/data/trajectory_all_14.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/trajectory_all_14.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/trajectory_all_14.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,40 @@
+MODEL 0
+ATOM 1 CA THR A 1 24.422 13.210 -4.270 1.00 1.00 A C
+ATOM 2 CB THR A 2 24.887 12.008 -3.448 1.00 1.00 A C
+ATOM 3 CA TRP A 3 22.624 15.829 -2.116 1.00 1.00 A C
+ATOM 4 CB TRP A 4 21.333 16.458 -2.648 1.00 1.00 A C
+ATOM 5 CA ILE A 5 23.196 15.863 1.663 1.00 1.00 A C
+ATOM 6 CB ILE A 6 24.553 15.743 2.422 1.00 1.00 A C
+ATOM 7 CA GLN A 7 20.058 17.420 3.035 1.00 1.00 A C
+ATOM 8 CB GLN A 8 18.831 16.791 2.350 1.00 1.00 A C
+ATOM 9 CA ASN A 9 19.770 19.885 5.821 1.00 1.00 A C
+ATOM 10 CB ASN A 10 20.807 20.908 6.076 1.00 1.00 A C
+ATOM 11 CA GLY A 11 16.963 22.270 4.795 1.00 1.00 A C
+ATOM 12 CA SER A 12 19.386 25.207 5.037 1.00 1.00 A C
+ATOM 13 CB SER A 13 19.722 25.960 6.309 1.00 1.00 A C
+ATOM 14 CA THR A 14 22.947 24.142 4.134 1.00 1.00 A C
+ATOM 15 CB THR A 15 24.233 24.523 5.036 1.00 1.00 A C
+ATOM 16 CA LYS A 16 22.673 21.495 1.497 1.00 1.00 A C
+ATOM 17 CB LYS A 17 21.694 21.485 0.262 1.00 1.00 A C
+ATOM 18 CA TRP A 18 25.962 19.675 0.755 1.00 1.00 A C
+ATOM 19 CB TRP A 19 26.511 18.752 1.914 1.00 1.00 A C
+ATOM 20 CA TYR A 20 27.125 17.980 -2.420 1.00 1.00 A C
+ATOM 21 CB TYR A 21 27.174 18.924 -3.665 1.00 1.00 A C
+ATOM 22 CA GLN A 22 28.785 14.662 -2.342 1.00 1.00 A C
+ATOM 23 CB GLN A 23 27.997 13.704 -1.466 1.00 1.00 A C
+ATOM 24 CA ASN A 24 30.874 12.584 -4.720 1.00 1.00 A C
+ATOM 25 CB ASN A 25 32.146 13.244 -5.162 1.00 1.00 A C
+ATOM 26 CA GLY A 26 29.992 9.290 -3.004 1.00 1.00 A C
+ATOM 27 CA SER A 27 31.881 10.055 0.268 1.00 1.00 A C
+ATOM 28 CB SER A 28 32.909 9.013 0.497 1.00 1.00 A C
+ATOM 29 CA THR A 29 34.162 13.086 -0.326 1.00 1.00 A C
+ATOM 30 CB THR A 30 35.395 12.827 -1.214 1.00 1.00 A C
+ATOM 31 CA LYS A 31 32.466 16.502 -0.373 1.00 1.00 A C
+ATOM 32 CB LYS A 32 31.741 17.017 0.877 1.00 1.00 A C
+ATOM 33 CA ILE A 33 32.805 19.002 -3.256 1.00 1.00 A C
+ATOM 34 CB ILE A 34 32.849 18.403 -4.576 1.00 1.00 A C
+ATOM 35 CA TYR A 35 30.292 21.512 -1.957 1.00 1.00 A C
+ATOM 36 CB TYR A 36 29.116 21.933 -2.923 1.00 1.00 A C
+ATOM 37 CA THR A 37 30.535 22.144 1.734 1.00 1.00 A C
+ATOM 38 CB THR A 38 31.890 22.569 2.417 1.00 1.00 A C
+ENDMDL
Added: SwiftApps/CMTS/stringmethod/src/data/trajectory_all_15.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/trajectory_all_15.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/trajectory_all_15.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,40 @@
+MODEL 0
+ATOM 1 CA THR A 1 24.249 12.885 -3.482 1.00 1.00 A C
+ATOM 2 CB THR A 2 24.740 11.675 -2.767 1.00 1.00 A C
+ATOM 3 CA TRP A 3 22.632 15.862 -1.801 1.00 1.00 A C
+ATOM 4 CB TRP A 4 21.541 16.677 -2.420 1.00 1.00 A C
+ATOM 5 CA ILE A 5 23.160 15.596 1.871 1.00 1.00 A C
+ATOM 6 CB ILE A 6 24.659 15.595 2.243 1.00 1.00 A C
+ATOM 7 CA GLN A 7 20.481 17.553 3.855 1.00 1.00 A C
+ATOM 8 CB GLN A 8 19.047 17.576 3.184 1.00 1.00 A C
+ATOM 9 CA ASN A 9 20.622 18.794 7.522 1.00 1.00 A C
+ATOM 10 CB ASN A 10 21.924 19.153 8.256 1.00 1.00 A C
+ATOM 11 CA GLY A 11 17.047 20.185 7.631 1.00 1.00 A C
+ATOM 12 CA SER A 12 17.652 23.644 6.004 1.00 1.00 A C
+ATOM 13 CB SER A 13 17.935 25.008 6.750 1.00 1.00 A C
+ATOM 14 CA THR A 14 21.142 22.976 4.870 1.00 1.00 A C
+ATOM 15 CB THR A 15 22.391 23.211 5.722 1.00 1.00 A C
+ATOM 16 CA LYS A 16 22.224 21.392 1.674 1.00 1.00 A C
+ATOM 17 CB LYS A 17 21.375 21.677 0.444 1.00 1.00 A C
+ATOM 18 CA TRP A 18 25.807 19.948 1.006 1.00 1.00 A C
+ATOM 19 CB TRP A 19 26.533 19.496 2.229 1.00 1.00 A C
+ATOM 20 CA TYR A 20 26.890 18.154 -2.137 1.00 1.00 A C
+ATOM 21 CB TYR A 21 27.210 19.139 -3.327 1.00 1.00 A C
+ATOM 22 CA GLN A 22 28.612 14.763 -2.258 1.00 1.00 A C
+ATOM 23 CB GLN A 23 28.181 13.747 -1.253 1.00 1.00 A C
+ATOM 24 CA ASN A 24 30.363 13.522 -5.358 1.00 1.00 A C
+ATOM 25 CB ASN A 25 31.129 14.511 -6.196 1.00 1.00 A C
+ATOM 26 CA GLY A 26 30.821 9.837 -4.897 1.00 1.00 A C
+ATOM 27 CA SER A 27 32.075 9.710 -1.313 1.00 1.00 A C
+ATOM 28 CB SER A 28 33.252 8.686 -1.406 1.00 1.00 A C
+ATOM 29 CA THR A 29 33.161 13.055 0.193 1.00 1.00 A C
+ATOM 30 CB THR A 30 34.709 13.222 0.356 1.00 1.00 A C
+ATOM 31 CA LYS A 31 31.680 16.401 0.674 1.00 1.00 A C
+ATOM 32 CB LYS A 32 31.108 16.685 2.095 1.00 1.00 A C
+ATOM 33 CA ILE A 33 32.952 19.269 -1.331 1.00 1.00 A C
+ATOM 34 CB ILE A 34 33.579 18.829 -2.673 1.00 1.00 A C
+ATOM 35 CA TYR A 35 30.315 21.875 -2.402 1.00 1.00 A C
+ATOM 36 CB TYR A 36 29.610 21.686 -3.689 1.00 1.00 A C
+ATOM 37 CA THR A 37 28.564 24.563 -0.415 1.00 1.00 A C
+ATOM 38 CB THR A 38 28.676 25.916 -1.022 1.00 1.00 A C
+ENDMDL
Added: SwiftApps/CMTS/stringmethod/src/data/trajectory_all_16.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/trajectory_all_16.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/trajectory_all_16.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,40 @@
+MODEL 0
+ATOM 1 CA THR A 1 23.974 12.646 -3.769 1.00 1.00 A C
+ATOM 2 CB THR A 2 23.919 11.357 -2.915 1.00 1.00 A C
+ATOM 3 CA TRP A 3 22.405 15.755 -2.083 1.00 1.00 A C
+ATOM 4 CB TRP A 4 21.417 16.657 -2.774 1.00 1.00 A C
+ATOM 5 CA ILE A 5 22.693 15.783 1.678 1.00 1.00 A C
+ATOM 6 CB ILE A 6 23.981 15.335 2.405 1.00 1.00 A C
+ATOM 7 CA GLN A 7 20.617 18.789 2.532 1.00 1.00 A C
+ATOM 8 CB GLN A 8 19.543 19.172 1.570 1.00 1.00 A C
+ATOM 9 CA ASN A 9 20.339 19.250 6.352 1.00 1.00 A C
+ATOM 10 CB ASN A 10 21.295 18.458 7.234 1.00 1.00 A C
+ATOM 11 CA GLY A 11 18.218 21.978 7.807 1.00 1.00 A C
+ATOM 12 CA SER A 12 19.448 24.513 5.234 1.00 1.00 A C
+ATOM 13 CB SER A 13 19.563 25.892 5.822 1.00 1.00 A C
+ATOM 14 CA THR A 14 22.971 23.244 4.508 1.00 1.00 A C
+ATOM 15 CB THR A 15 24.015 23.197 5.659 1.00 1.00 A C
+ATOM 16 CA LYS A 16 23.438 21.510 1.236 1.00 1.00 A C
+ATOM 17 CB LYS A 17 22.503 21.955 0.078 1.00 1.00 A C
+ATOM 18 CA TRP A 18 26.523 19.434 0.960 1.00 1.00 A C
+ATOM 19 CB TRP A 19 27.192 18.681 2.077 1.00 1.00 A C
+ATOM 20 CA TYR A 20 27.193 17.309 -2.223 1.00 1.00 A C
+ATOM 21 CB TYR A 21 27.174 18.047 -3.595 1.00 1.00 A C
+ATOM 22 CA GLN A 22 28.595 13.899 -2.045 1.00 1.00 A C
+ATOM 23 CB GLN A 23 27.894 12.798 -1.147 1.00 1.00 A C
+ATOM 24 CA ASN A 24 30.657 13.367 -5.167 1.00 1.00 A C
+ATOM 25 CB ASN A 25 31.701 14.388 -5.417 1.00 1.00 A C
+ATOM 26 CA GLY A 26 31.134 9.682 -4.332 1.00 1.00 A C
+ATOM 27 CA SER A 27 32.411 9.712 -0.758 1.00 1.00 A C
+ATOM 28 CB SER A 28 33.490 8.747 -0.449 1.00 1.00 A C
+ATOM 29 CA THR A 29 33.605 13.262 -0.309 1.00 1.00 A C
+ATOM 30 CB THR A 30 34.949 13.695 -0.805 1.00 1.00 A C
+ATOM 31 CA LYS A 31 31.182 15.927 0.608 1.00 1.00 A C
+ATOM 32 CB LYS A 32 30.405 16.069 1.884 1.00 1.00 A C
+ATOM 33 CA ILE A 33 31.794 19.283 -1.201 1.00 1.00 A C
+ATOM 34 CB ILE A 34 32.484 19.491 -2.541 1.00 1.00 A C
+ATOM 35 CA TYR A 35 29.858 22.455 -0.484 1.00 1.00 A C
+ATOM 36 CB TYR A 36 29.883 23.429 0.686 1.00 1.00 A C
+ATOM 37 CA THR A 37 27.716 23.614 -3.365 1.00 1.00 A C
+ATOM 38 CB THR A 38 27.701 22.850 -4.690 1.00 1.00 A C
+ENDMDL
Added: SwiftApps/CMTS/stringmethod/src/data/trajectory_all_17.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/trajectory_all_17.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/trajectory_all_17.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,40 @@
+MODEL 0
+ATOM 1 CA THR A 1 23.994 12.669 -4.114 1.00 1.00 A C
+ATOM 2 CB THR A 2 24.198 11.588 -3.127 1.00 1.00 A C
+ATOM 3 CA TRP A 3 22.205 15.504 -2.590 1.00 1.00 A C
+ATOM 4 CB TRP A 4 20.809 16.070 -2.965 1.00 1.00 A C
+ATOM 5 CA ILE A 5 22.559 15.626 1.193 1.00 1.00 A C
+ATOM 6 CB ILE A 6 23.782 15.187 2.108 1.00 1.00 A C
+ATOM 7 CA GLN A 7 19.754 18.051 1.930 1.00 1.00 A C
+ATOM 8 CB GLN A 8 18.537 18.201 0.975 1.00 1.00 A C
+ATOM 9 CA ASN A 9 19.998 19.217 5.493 1.00 1.00 A C
+ATOM 10 CB ASN A 10 21.285 18.847 6.363 1.00 1.00 A C
+ATOM 11 CA GLY A 11 17.487 21.861 5.194 1.00 1.00 A C
+ATOM 12 CA SER A 12 19.728 24.996 4.967 1.00 1.00 A C
+ATOM 13 CB SER A 13 19.861 26.009 6.050 1.00 1.00 A C
+ATOM 14 CA THR A 14 23.338 23.453 5.222 1.00 1.00 A C
+ATOM 15 CB THR A 15 24.043 23.397 6.580 1.00 1.00 A C
+ATOM 16 CA LYS A 16 23.152 21.149 2.408 1.00 1.00 A C
+ATOM 17 CB LYS A 17 21.935 21.295 1.574 1.00 1.00 A C
+ATOM 18 CA TRP A 18 26.287 19.339 0.930 1.00 1.00 A C
+ATOM 19 CB TRP A 19 27.193 18.397 1.746 1.00 1.00 A C
+ATOM 20 CA TYR A 20 26.894 17.702 -2.411 1.00 1.00 A C
+ATOM 21 CB TYR A 21 27.259 18.593 -3.508 1.00 1.00 A C
+ATOM 22 CA GLN A 22 28.429 14.246 -2.174 1.00 1.00 A C
+ATOM 23 CB GLN A 23 27.869 13.045 -1.331 1.00 1.00 A C
+ATOM 24 CA ASN A 24 31.096 13.695 -4.735 1.00 1.00 A C
+ATOM 25 CB ASN A 25 32.200 14.755 -5.010 1.00 1.00 A C
+ATOM 26 CA GLY A 26 31.045 9.948 -4.411 1.00 1.00 A C
+ATOM 27 CA SER A 27 33.058 9.644 -1.217 1.00 1.00 A C
+ATOM 28 CB SER A 28 34.282 8.777 -1.292 1.00 1.00 A C
+ATOM 29 CA THR A 29 33.804 13.308 -0.388 1.00 1.00 A C
+ATOM 30 CB THR A 30 34.913 14.165 -1.175 1.00 1.00 A C
+ATOM 31 CA LYS A 31 31.001 15.374 1.058 1.00 1.00 A C
+ATOM 32 CB LYS A 32 30.399 14.916 2.385 1.00 1.00 A C
+ATOM 33 CA ILE A 33 31.678 18.928 0.193 1.00 1.00 A C
+ATOM 34 CB ILE A 34 32.851 19.176 -0.809 1.00 1.00 A C
+ATOM 35 CA TYR A 35 29.936 22.295 -0.013 1.00 1.00 A C
+ATOM 36 CB TYR A 36 29.848 23.193 1.214 1.00 1.00 A C
+ATOM 37 CA THR A 37 29.753 23.181 -3.710 1.00 1.00 A C
+ATOM 38 CB THR A 38 29.681 22.096 -4.812 1.00 1.00 A C
+ENDMDL
Added: SwiftApps/CMTS/stringmethod/src/data/trajectory_all_18.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/trajectory_all_18.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/trajectory_all_18.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,40 @@
+MODEL 0
+ATOM 1 CA THR A 1 24.215 12.473 -4.133 1.00 1.00 A C
+ATOM 2 CB THR A 2 24.535 11.192 -3.335 1.00 1.00 A C
+ATOM 3 CA TRP A 3 22.396 15.422 -2.396 1.00 1.00 A C
+ATOM 4 CB TRP A 4 21.418 16.408 -3.001 1.00 1.00 A C
+ATOM 5 CA ILE A 5 22.572 15.614 1.424 1.00 1.00 A C
+ATOM 6 CB ILE A 6 23.741 14.993 2.165 1.00 1.00 A C
+ATOM 7 CA GLN A 7 20.158 18.403 2.196 1.00 1.00 A C
+ATOM 8 CB GLN A 8 19.110 18.783 1.151 1.00 1.00 A C
+ATOM 9 CA ASN A 9 19.425 19.100 5.826 1.00 1.00 A C
+ATOM 10 CB ASN A 10 20.398 18.656 6.900 1.00 1.00 A C
+ATOM 11 CA GLY A 11 16.946 21.960 5.760 1.00 1.00 A C
+ATOM 12 CA SER A 12 19.332 25.036 5.613 1.00 1.00 A C
+ATOM 13 CB SER A 13 19.599 26.055 6.638 1.00 1.00 A C
+ATOM 14 CA THR A 14 22.638 23.196 5.183 1.00 1.00 A C
+ATOM 15 CB THR A 15 23.637 22.837 6.295 1.00 1.00 A C
+ATOM 16 CA LYS A 16 22.996 21.704 1.767 1.00 1.00 A C
+ATOM 17 CB LYS A 17 22.288 22.146 0.460 1.00 1.00 A C
+ATOM 18 CA TRP A 18 25.821 19.583 0.465 1.00 1.00 A C
+ATOM 19 CB TRP A 19 26.528 18.827 1.589 1.00 1.00 A C
+ATOM 20 CA TYR A 20 26.899 17.351 -2.415 1.00 1.00 A C
+ATOM 21 CB TYR A 21 27.192 18.169 -3.730 1.00 1.00 A C
+ATOM 22 CA GLN A 22 28.541 14.014 -2.054 1.00 1.00 A C
+ATOM 23 CB GLN A 23 27.893 13.008 -1.183 1.00 1.00 A C
+ATOM 24 CA ASN A 24 30.636 13.738 -5.155 1.00 1.00 A C
+ATOM 25 CB ASN A 25 31.651 14.809 -5.663 1.00 1.00 A C
+ATOM 26 CA GLY A 26 31.084 10.047 -4.798 1.00 1.00 A C
+ATOM 27 CA SER A 27 33.402 9.701 -1.822 1.00 1.00 A C
+ATOM 28 CB SER A 28 34.701 8.912 -2.004 1.00 1.00 A C
+ATOM 29 CA THR A 29 34.217 13.328 -0.984 1.00 1.00 A C
+ATOM 30 CB THR A 30 35.170 14.094 -1.985 1.00 1.00 A C
+ATOM 31 CA LYS A 31 31.736 15.865 0.674 1.00 1.00 A C
+ATOM 32 CB LYS A 32 31.398 15.581 2.158 1.00 1.00 A C
+ATOM 33 CA ILE A 33 31.492 19.195 -1.052 1.00 1.00 A C
+ATOM 34 CB ILE A 34 31.708 19.201 -2.603 1.00 1.00 A C
+ATOM 35 CA TYR A 35 29.853 22.519 0.083 1.00 1.00 A C
+ATOM 36 CB TYR A 36 30.375 23.600 0.928 1.00 1.00 A C
+ATOM 37 CA THR A 37 27.113 23.654 -2.460 1.00 1.00 A C
+ATOM 38 CB THR A 38 26.216 22.543 -3.164 1.00 1.00 A C
+ENDMDL
Added: SwiftApps/CMTS/stringmethod/src/data/trajectory_all_19.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/trajectory_all_19.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/trajectory_all_19.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,40 @@
+MODEL 0
+ATOM 1 CA THR A 1 24.425 12.824 -3.856 1.00 1.00 A C
+ATOM 2 CB THR A 2 24.260 11.546 -2.996 1.00 1.00 A C
+ATOM 3 CA TRP A 3 22.623 15.909 -2.416 1.00 1.00 A C
+ATOM 4 CB TRP A 4 21.500 16.768 -3.051 1.00 1.00 A C
+ATOM 5 CA ILE A 5 22.456 15.514 1.338 1.00 1.00 A C
+ATOM 6 CB ILE A 6 23.708 15.254 2.234 1.00 1.00 A C
+ATOM 7 CA GLN A 7 19.671 17.868 2.550 1.00 1.00 A C
+ATOM 8 CB GLN A 8 18.474 18.133 1.604 1.00 1.00 A C
+ATOM 9 CA ASN A 9 19.525 19.046 6.053 1.00 1.00 A C
+ATOM 10 CB ASN A 10 20.700 18.714 6.952 1.00 1.00 A C
+ATOM 11 CA GLY A 11 17.165 21.897 6.317 1.00 1.00 A C
+ATOM 12 CA SER A 12 18.676 24.410 3.980 1.00 1.00 A C
+ATOM 13 CB SER A 13 18.181 25.756 4.422 1.00 1.00 A C
+ATOM 14 CA THR A 14 22.359 23.490 3.771 1.00 1.00 A C
+ATOM 15 CB THR A 15 23.447 23.721 4.842 1.00 1.00 A C
+ATOM 16 CA LYS A 16 22.869 20.925 1.087 1.00 1.00 A C
+ATOM 17 CB LYS A 17 22.032 20.833 -0.292 1.00 1.00 A C
+ATOM 18 CA TRP A 18 26.241 19.231 0.929 1.00 1.00 A C
+ATOM 19 CB TRP A 19 26.878 18.376 2.046 1.00 1.00 A C
+ATOM 20 CA TYR A 20 27.373 17.821 -2.507 1.00 1.00 A C
+ATOM 21 CB TYR A 21 27.614 18.728 -3.742 1.00 1.00 A C
+ATOM 22 CA GLN A 22 28.673 14.261 -2.089 1.00 1.00 A C
+ATOM 23 CB GLN A 23 27.896 13.227 -1.358 1.00 1.00 A C
+ATOM 24 CA ASN A 24 30.929 12.848 -4.773 1.00 1.00 A C
+ATOM 25 CB ASN A 25 31.703 13.728 -5.735 1.00 1.00 A C
+ATOM 26 CA GLY A 26 31.377 9.667 -2.959 1.00 1.00 A C
+ATOM 27 CA SER A 27 33.926 10.130 -0.373 1.00 1.00 A C
+ATOM 28 CB SER A 28 35.185 9.253 -0.409 1.00 1.00 A C
+ATOM 29 CA THR A 29 34.390 13.832 -0.730 1.00 1.00 A C
+ATOM 30 CB THR A 30 35.457 14.478 -1.650 1.00 1.00 A C
+ATOM 31 CA LYS A 31 31.886 16.587 0.129 1.00 1.00 A C
+ATOM 32 CB LYS A 32 31.162 16.366 1.409 1.00 1.00 A C
+ATOM 33 CA ILE A 33 31.398 20.060 -1.263 1.00 1.00 A C
+ATOM 34 CB ILE A 34 31.225 20.332 -2.777 1.00 1.00 A C
+ATOM 35 CA TYR A 35 29.572 22.709 0.941 1.00 1.00 A C
+ATOM 36 CB TYR A 36 30.244 23.440 2.224 1.00 1.00 A C
+ATOM 37 CA THR A 37 27.090 23.804 -1.765 1.00 1.00 A C
+ATOM 38 CB THR A 38 26.401 22.713 -2.573 1.00 1.00 A C
+ENDMDL
Added: SwiftApps/CMTS/stringmethod/src/data/trajectory_all_2.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/trajectory_all_2.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/trajectory_all_2.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,40 @@
+MODEL 0
+ATOM 1 CA THR A 1 24.961 14.402 -5.078 1.00 1.00 A C
+ATOM 2 CB THR A 2 24.840 12.986 -4.497 1.00 1.00 A C
+ATOM 3 CA TRP A 3 23.326 17.516 -3.560 1.00 1.00 A C
+ATOM 4 CB TRP A 4 22.788 18.663 -4.465 1.00 1.00 A C
+ATOM 5 CA ILE A 5 21.774 16.387 -0.280 1.00 1.00 A C
+ATOM 6 CB ILE A 6 22.448 15.530 0.834 1.00 1.00 A C
+ATOM 7 CA GLN A 7 18.856 18.298 1.245 1.00 1.00 A C
+ATOM 8 CB GLN A 8 17.469 18.584 0.759 1.00 1.00 A C
+ATOM 9 CA ASN A 9 18.857 19.202 4.845 1.00 1.00 A C
+ATOM 10 CB ASN A 10 20.186 19.489 5.607 1.00 1.00 A C
+ATOM 11 CA GLY A 11 15.658 21.079 5.005 1.00 1.00 A C
+ATOM 12 CA SER A 12 16.550 24.118 3.000 1.00 1.00 A C
+ATOM 13 CB SER A 13 15.592 25.314 3.428 1.00 1.00 A C
+ATOM 14 CA THR A 14 20.320 24.447 3.425 1.00 1.00 A C
+ATOM 15 CB THR A 15 20.999 24.599 4.827 1.00 1.00 A C
+ATOM 16 CA LYS A 16 21.217 22.234 0.471 1.00 1.00 A C
+ATOM 17 CB LYS A 17 20.161 22.098 -0.624 1.00 1.00 A C
+ATOM 18 CA TRP A 18 24.823 21.102 0.195 1.00 1.00 A C
+ATOM 19 CB TRP A 19 25.478 21.308 1.542 1.00 1.00 A C
+ATOM 20 CA TYR A 20 27.089 18.698 -1.680 1.00 1.00 A C
+ATOM 21 CB TYR A 21 28.142 19.276 -2.679 1.00 1.00 A C
+ATOM 22 CA GLN A 22 27.993 15.101 -0.654 1.00 1.00 A C
+ATOM 23 CB GLN A 23 26.995 14.303 0.084 1.00 1.00 A C
+ATOM 24 CA ASN A 24 30.244 12.749 -2.689 1.00 1.00 A C
+ATOM 25 CB ASN A 25 31.090 13.362 -3.876 1.00 1.00 A C
+ATOM 26 CA GLY A 26 31.427 9.440 -1.434 1.00 1.00 A C
+ATOM 27 CA SER A 27 32.110 10.061 2.262 1.00 1.00 A C
+ATOM 28 CB SER A 28 32.157 8.736 3.066 1.00 1.00 A C
+ATOM 29 CA THR A 29 34.894 12.557 1.844 1.00 1.00 A C
+ATOM 30 CB THR A 30 36.112 12.005 1.092 1.00 1.00 A C
+ATOM 31 CA LYS A 31 34.023 15.552 -0.444 1.00 1.00 A C
+ATOM 32 CB LYS A 32 34.297 15.544 -1.947 1.00 1.00 A C
+ATOM 33 CA ILE A 33 31.204 17.202 1.406 1.00 1.00 A C
+ATOM 34 CB ILE A 34 30.753 16.866 2.862 1.00 1.00 A C
+ATOM 35 CA TYR A 35 30.968 20.902 0.263 1.00 1.00 A C
+ATOM 36 CB TYR A 36 31.424 21.248 -1.149 1.00 1.00 A C
+ATOM 37 CA THR A 37 28.911 23.272 2.228 1.00 1.00 A C
+ATOM 38 CB THR A 38 29.258 23.737 3.691 1.00 1.00 A C
+ENDMDL
Added: SwiftApps/CMTS/stringmethod/src/data/trajectory_all_20.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/trajectory_all_20.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/trajectory_all_20.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,40 @@
+MODEL 0
+ATOM 1 CA THR A 1 23.796 12.698 -4.365 1.00 1.00 A C
+ATOM 2 CB THR A 2 24.151 11.597 -3.399 1.00 1.00 A C
+ATOM 3 CA TRP A 3 22.321 15.518 -2.381 1.00 1.00 A C
+ATOM 4 CB TRP A 4 21.441 16.525 -3.064 1.00 1.00 A C
+ATOM 5 CA ILE A 5 22.098 15.635 1.428 1.00 1.00 A C
+ATOM 6 CB ILE A 6 23.110 15.393 2.464 1.00 1.00 A C
+ATOM 7 CA GLN A 7 19.542 18.422 2.115 1.00 1.00 A C
+ATOM 8 CB GLN A 8 18.259 18.313 1.386 1.00 1.00 A C
+ATOM 9 CA ASN A 9 20.160 19.757 5.751 1.00 1.00 A C
+ATOM 10 CB ASN A 10 21.554 19.686 6.359 1.00 1.00 A C
+ATOM 11 CA GLY A 11 17.413 22.395 5.776 1.00 1.00 A C
+ATOM 12 CA SER A 12 19.247 25.343 4.428 1.00 1.00 A C
+ATOM 13 CB SER A 13 19.239 26.616 5.202 1.00 1.00 A C
+ATOM 14 CA THR A 14 22.691 23.757 4.195 1.00 1.00 A C
+ATOM 15 CB THR A 15 23.598 23.642 5.460 1.00 1.00 A C
+ATOM 16 CA LYS A 16 23.467 22.015 1.009 1.00 1.00 A C
+ATOM 17 CB LYS A 17 23.095 22.707 -0.258 1.00 1.00 A C
+ATOM 18 CA TRP A 18 25.721 18.981 0.747 1.00 1.00 A C
+ATOM 19 CB TRP A 19 25.460 18.027 1.854 1.00 1.00 A C
+ATOM 20 CA TYR A 20 26.749 17.159 -2.453 1.00 1.00 A C
+ATOM 21 CB TYR A 21 27.136 18.175 -3.598 1.00 1.00 A C
+ATOM 22 CA GLN A 22 28.625 13.804 -3.014 1.00 1.00 A C
+ATOM 23 CB GLN A 23 27.784 12.706 -2.267 1.00 1.00 A C
+ATOM 24 CA ASN A 24 31.458 12.325 -5.085 1.00 1.00 A C
+ATOM 25 CB ASN A 25 32.454 13.221 -5.763 1.00 1.00 A C
+ATOM 26 CA GLY A 26 32.120 9.035 -3.395 1.00 1.00 A C
+ATOM 27 CA SER A 27 33.491 9.574 0.058 1.00 1.00 A C
+ATOM 28 CB SER A 28 34.712 8.931 0.629 1.00 1.00 A C
+ATOM 29 CA THR A 29 34.191 13.320 -0.646 1.00 1.00 A C
+ATOM 30 CB THR A 30 35.176 13.719 -1.736 1.00 1.00 A C
+ATOM 31 CA LYS A 31 31.545 15.739 0.660 1.00 1.00 A C
+ATOM 32 CB LYS A 32 31.277 15.902 2.158 1.00 1.00 A C
+ATOM 33 CA ILE A 33 31.071 18.971 -1.167 1.00 1.00 A C
+ATOM 34 CB ILE A 34 31.098 19.122 -2.730 1.00 1.00 A C
+ATOM 35 CA TYR A 35 29.333 21.665 0.855 1.00 1.00 A C
+ATOM 36 CB TYR A 36 29.959 22.159 2.155 1.00 1.00 A C
+ATOM 37 CA THR A 37 27.745 24.005 -1.718 1.00 1.00 A C
+ATOM 38 CB THR A 38 26.750 23.599 -2.695 1.00 1.00 A C
+ENDMDL
Added: SwiftApps/CMTS/stringmethod/src/data/trajectory_all_21.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/trajectory_all_21.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/trajectory_all_21.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,40 @@
+MODEL 0
+ATOM 1 CA THR A 1 24.421 12.601 -4.540 1.00 1.00 A C
+ATOM 2 CB THR A 2 24.764 11.399 -3.736 1.00 1.00 A C
+ATOM 3 CA TRP A 3 22.648 15.306 -2.629 1.00 1.00 A C
+ATOM 4 CB TRP A 4 21.594 16.092 -3.330 1.00 1.00 A C
+ATOM 5 CA ILE A 5 22.135 15.373 1.245 1.00 1.00 A C
+ATOM 6 CB ILE A 6 23.241 14.774 2.228 1.00 1.00 A C
+ATOM 7 CA GLN A 7 19.769 18.186 1.742 1.00 1.00 A C
+ATOM 8 CB GLN A 8 18.457 18.256 0.906 1.00 1.00 A C
+ATOM 9 CA ASN A 9 19.623 19.863 5.158 1.00 1.00 A C
+ATOM 10 CB ASN A 10 20.868 19.569 6.021 1.00 1.00 A C
+ATOM 11 CA GLY A 11 17.847 23.215 4.417 1.00 1.00 A C
+ATOM 12 CA SER A 12 20.497 25.841 3.981 1.00 1.00 A C
+ATOM 13 CB SER A 13 20.453 27.050 4.884 1.00 1.00 A C
+ATOM 14 CA THR A 14 23.344 23.469 4.511 1.00 1.00 A C
+ATOM 15 CB THR A 15 23.726 22.959 5.961 1.00 1.00 A C
+ATOM 16 CA LYS A 16 23.188 21.393 1.284 1.00 1.00 A C
+ATOM 17 CB LYS A 17 22.515 21.819 0.069 1.00 1.00 A C
+ATOM 18 CA TRP A 18 25.844 18.781 1.081 1.00 1.00 A C
+ATOM 19 CB TRP A 19 26.164 17.925 2.314 1.00 1.00 A C
+ATOM 20 CA TYR A 20 27.090 17.542 -2.351 1.00 1.00 A C
+ATOM 21 CB TYR A 21 27.541 18.324 -3.554 1.00 1.00 A C
+ATOM 22 CA GLN A 22 28.467 13.932 -1.707 1.00 1.00 A C
+ATOM 23 CB GLN A 23 27.734 12.961 -0.972 1.00 1.00 A C
+ATOM 24 CA ASN A 24 30.910 13.427 -4.619 1.00 1.00 A C
+ATOM 25 CB ASN A 25 32.058 14.377 -4.915 1.00 1.00 A C
+ATOM 26 CA GLY A 26 30.914 9.672 -3.778 1.00 1.00 A C
+ATOM 27 CA SER A 27 32.670 10.371 -0.446 1.00 1.00 A C
+ATOM 28 CB SER A 28 33.751 9.380 -0.046 1.00 1.00 A C
+ATOM 29 CA THR A 29 33.742 13.936 -0.848 1.00 1.00 A C
+ATOM 30 CB THR A 30 34.708 14.486 -1.929 1.00 1.00 A C
+ATOM 31 CA LYS A 31 31.659 16.441 1.058 1.00 1.00 A C
+ATOM 32 CB LYS A 32 31.649 16.276 2.590 1.00 1.00 A C
+ATOM 33 CA ILE A 33 31.515 19.599 -1.080 1.00 1.00 A C
+ATOM 34 CB ILE A 34 31.400 19.416 -2.696 1.00 1.00 A C
+ATOM 35 CA TYR A 35 29.618 22.544 0.399 1.00 1.00 A C
+ATOM 36 CB TYR A 36 30.295 23.386 1.502 1.00 1.00 A C
+ATOM 37 CA THR A 37 26.738 23.794 -1.692 1.00 1.00 A C
+ATOM 38 CB THR A 38 25.993 22.870 -2.745 1.00 1.00 A C
+ENDMDL
Added: SwiftApps/CMTS/stringmethod/src/data/trajectory_all_22.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/trajectory_all_22.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/trajectory_all_22.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,40 @@
+MODEL 0
+ATOM 1 CA THR A 1 24.376 12.965 -4.657 1.00 1.00 A C
+ATOM 2 CB THR A 2 24.552 11.611 -3.988 1.00 1.00 A C
+ATOM 3 CA TRP A 3 22.753 15.275 -2.090 1.00 1.00 A C
+ATOM 4 CB TRP A 4 21.811 16.389 -2.535 1.00 1.00 A C
+ATOM 5 CA ILE A 5 22.532 15.422 1.639 1.00 1.00 A C
+ATOM 6 CB ILE A 6 23.790 15.473 2.596 1.00 1.00 A C
+ATOM 7 CA GLN A 7 19.314 17.329 1.431 1.00 1.00 A C
+ATOM 8 CB GLN A 8 18.226 17.084 0.318 1.00 1.00 A C
+ATOM 9 CA ASN A 9 18.147 18.856 4.570 1.00 1.00 A C
+ATOM 10 CB ASN A 10 19.363 19.101 5.477 1.00 1.00 A C
+ATOM 11 CA GLY A 11 16.946 22.548 4.277 1.00 1.00 A C
+ATOM 12 CA SER A 12 19.836 24.976 5.005 1.00 1.00 A C
+ATOM 13 CB SER A 13 19.946 25.823 6.234 1.00 1.00 A C
+ATOM 14 CA THR A 14 22.562 22.261 5.055 1.00 1.00 A C
+ATOM 15 CB THR A 15 22.672 21.170 6.244 1.00 1.00 A C
+ATOM 16 CA LYS A 16 23.540 21.744 1.449 1.00 1.00 A C
+ATOM 17 CB LYS A 17 23.227 22.986 0.679 1.00 1.00 A C
+ATOM 18 CA TRP A 18 26.349 19.113 0.919 1.00 1.00 A C
+ATOM 19 CB TRP A 19 26.897 18.217 2.019 1.00 1.00 A C
+ATOM 20 CA TYR A 20 27.207 17.625 -2.490 1.00 1.00 A C
+ATOM 21 CB TYR A 21 27.442 18.460 -3.698 1.00 1.00 A C
+ATOM 22 CA GLN A 22 28.853 14.265 -2.070 1.00 1.00 A C
+ATOM 23 CB GLN A 23 28.188 13.457 -0.983 1.00 1.00 A C
+ATOM 24 CA ASN A 24 30.983 13.140 -4.877 1.00 1.00 A C
+ATOM 25 CB ASN A 25 31.712 14.307 -5.433 1.00 1.00 A C
+ATOM 26 CA GLY A 26 31.718 9.536 -4.086 1.00 1.00 A C
+ATOM 27 CA SER A 27 33.175 9.844 -0.597 1.00 1.00 A C
+ATOM 28 CB SER A 28 34.079 8.696 -0.085 1.00 1.00 A C
+ATOM 29 CA THR A 29 34.362 13.434 -0.780 1.00 1.00 A C
+ATOM 30 CB THR A 30 35.408 13.779 -1.775 1.00 1.00 A C
+ATOM 31 CA LYS A 31 31.976 16.151 0.518 1.00 1.00 A C
+ATOM 32 CB LYS A 32 31.022 15.969 1.782 1.00 1.00 A C
+ATOM 33 CA ILE A 33 32.225 19.740 -0.588 1.00 1.00 A C
+ATOM 34 CB ILE A 34 32.927 20.244 -1.922 1.00 1.00 A C
+ATOM 35 CA TYR A 35 29.792 22.514 0.032 1.00 1.00 A C
+ATOM 36 CB TYR A 36 29.901 23.254 1.325 1.00 1.00 A C
+ATOM 37 CA THR A 37 27.636 23.934 -2.835 1.00 1.00 A C
+ATOM 38 CB THR A 38 27.653 22.843 -3.877 1.00 1.00 A C
+ENDMDL
Added: SwiftApps/CMTS/stringmethod/src/data/trajectory_all_23.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/trajectory_all_23.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/trajectory_all_23.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,40 @@
+MODEL 0
+ATOM 1 CA THR A 1 24.493 13.118 -4.697 1.00 1.00 A C
+ATOM 2 CB THR A 2 24.648 11.784 -3.882 1.00 1.00 A C
+ATOM 3 CA TRP A 3 22.509 15.855 -2.932 1.00 1.00 A C
+ATOM 4 CB TRP A 4 21.339 16.531 -3.607 1.00 1.00 A C
+ATOM 5 CA ILE A 5 21.910 15.322 0.811 1.00 1.00 A C
+ATOM 6 CB ILE A 6 23.001 14.559 1.694 1.00 1.00 A C
+ATOM 7 CA GLN A 7 19.808 18.374 1.172 1.00 1.00 A C
+ATOM 8 CB GLN A 8 18.993 18.621 -0.086 1.00 1.00 A C
+ATOM 9 CA ASN A 9 18.951 19.330 4.624 1.00 1.00 A C
+ATOM 10 CB ASN A 10 19.402 18.472 5.782 1.00 1.00 A C
+ATOM 11 CA GLY A 11 17.507 22.777 4.510 1.00 1.00 A C
+ATOM 12 CA SER A 12 20.332 25.340 4.071 1.00 1.00 A C
+ATOM 13 CB SER A 13 20.480 26.445 5.167 1.00 1.00 A C
+ATOM 14 CA THR A 14 23.114 22.651 4.514 1.00 1.00 A C
+ATOM 15 CB THR A 15 23.462 21.922 5.832 1.00 1.00 A C
+ATOM 16 CA LYS A 16 23.399 20.943 1.123 1.00 1.00 A C
+ATOM 17 CB LYS A 17 22.900 21.697 -0.041 1.00 1.00 A C
+ATOM 18 CA TRP A 18 25.953 18.205 0.895 1.00 1.00 A C
+ATOM 19 CB TRP A 19 26.077 17.110 1.958 1.00 1.00 A C
+ATOM 20 CA TYR A 20 27.104 17.381 -2.591 1.00 1.00 A C
+ATOM 21 CB TYR A 21 27.679 18.390 -3.585 1.00 1.00 A C
+ATOM 22 CA GLN A 22 28.740 14.057 -1.586 1.00 1.00 A C
+ATOM 23 CB GLN A 23 28.135 13.097 -0.497 1.00 1.00 A C
+ATOM 24 CA ASN A 24 30.900 12.858 -4.648 1.00 1.00 A C
+ATOM 25 CB ASN A 25 31.408 13.994 -5.605 1.00 1.00 A C
+ATOM 26 CA GLY A 26 32.565 9.531 -4.033 1.00 1.00 A C
+ATOM 27 CA SER A 27 33.853 10.078 -0.619 1.00 1.00 A C
+ATOM 28 CB SER A 28 35.201 9.537 -0.419 1.00 1.00 A C
+ATOM 29 CA THR A 29 34.453 13.855 -0.363 1.00 1.00 A C
+ATOM 30 CB THR A 30 35.287 14.613 -1.465 1.00 1.00 A C
+ATOM 31 CA LYS A 31 31.540 15.997 1.100 1.00 1.00 A C
+ATOM 32 CB LYS A 32 30.712 15.829 2.291 1.00 1.00 A C
+ATOM 33 CA ILE A 33 31.327 19.374 -0.438 1.00 1.00 A C
+ATOM 34 CB ILE A 34 31.532 19.545 -1.950 1.00 1.00 A C
+ATOM 35 CA TYR A 35 29.226 22.242 1.139 1.00 1.00 A C
+ATOM 36 CB TYR A 36 29.720 22.993 2.347 1.00 1.00 A C
+ATOM 37 CA THR A 37 27.063 24.177 -1.291 1.00 1.00 A C
+ATOM 38 CB THR A 38 26.158 23.618 -2.370 1.00 1.00 A C
+ENDMDL
Added: SwiftApps/CMTS/stringmethod/src/data/trajectory_all_24.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/trajectory_all_24.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/trajectory_all_24.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,40 @@
+MODEL 0
+ATOM 1 CA THR A 1 24.085 12.836 -4.458 1.00 1.00 A C
+ATOM 2 CB THR A 2 24.254 11.688 -3.526 1.00 1.00 A C
+ATOM 3 CA TRP A 3 22.350 15.992 -3.440 1.00 1.00 A C
+ATOM 4 CB TRP A 4 21.300 16.696 -4.351 1.00 1.00 A C
+ATOM 5 CA ILE A 5 21.961 15.405 0.355 1.00 1.00 A C
+ATOM 6 CB ILE A 6 22.741 14.517 1.428 1.00 1.00 A C
+ATOM 7 CA GLN A 7 20.180 18.490 1.416 1.00 1.00 A C
+ATOM 8 CB GLN A 8 19.214 19.364 0.542 1.00 1.00 A C
+ATOM 9 CA ASN A 9 19.892 18.336 5.089 1.00 1.00 A C
+ATOM 10 CB ASN A 10 21.046 17.623 5.950 1.00 1.00 A C
+ATOM 11 CA GLY A 11 17.536 21.177 5.668 1.00 1.00 A C
+ATOM 12 CA SER A 12 19.603 24.328 5.580 1.00 1.00 A C
+ATOM 13 CB SER A 13 19.511 25.444 6.669 1.00 1.00 A C
+ATOM 14 CA THR A 14 23.019 22.837 5.046 1.00 1.00 A C
+ATOM 15 CB THR A 15 23.920 22.151 6.099 1.00 1.00 A C
+ATOM 16 CA LYS A 16 23.602 22.070 1.445 1.00 1.00 A C
+ATOM 17 CB LYS A 17 23.358 23.187 0.375 1.00 1.00 A C
+ATOM 18 CA TRP A 18 25.648 19.061 0.454 1.00 1.00 A C
+ATOM 19 CB TRP A 19 25.732 17.865 1.375 1.00 1.00 A C
+ATOM 20 CA TYR A 20 26.818 17.724 -2.825 1.00 1.00 A C
+ATOM 21 CB TYR A 21 27.305 18.470 -4.078 1.00 1.00 A C
+ATOM 22 CA GLN A 22 28.658 14.472 -1.910 1.00 1.00 A C
+ATOM 23 CB GLN A 23 28.268 13.591 -0.760 1.00 1.00 A C
+ATOM 24 CA ASN A 24 30.973 13.018 -4.601 1.00 1.00 A C
+ATOM 25 CB ASN A 25 32.078 13.780 -5.158 1.00 1.00 A C
+ATOM 26 CA GLY A 26 30.525 9.504 -3.135 1.00 1.00 A C
+ATOM 27 CA SER A 27 32.914 9.633 -0.118 1.00 1.00 A C
+ATOM 28 CB SER A 28 34.176 8.788 -0.191 1.00 1.00 A C
+ATOM 29 CA THR A 29 33.980 13.409 -0.409 1.00 1.00 A C
+ATOM 30 CB THR A 30 35.041 13.752 -1.371 1.00 1.00 A C
+ATOM 31 CA LYS A 31 31.924 16.390 1.089 1.00 1.00 A C
+ATOM 32 CB LYS A 32 31.646 16.520 2.620 1.00 1.00 A C
+ATOM 33 CA ILE A 33 31.183 19.462 -1.038 1.00 1.00 A C
+ATOM 34 CB ILE A 34 31.080 19.315 -2.606 1.00 1.00 A C
+ATOM 35 CA TYR A 35 29.391 22.295 0.744 1.00 1.00 A C
+ATOM 36 CB TYR A 36 30.163 23.052 1.860 1.00 1.00 A C
+ATOM 37 CA THR A 37 27.224 23.985 -1.885 1.00 1.00 A C
+ATOM 38 CB THR A 38 25.979 23.502 -2.675 1.00 1.00 A C
+ENDMDL
Added: SwiftApps/CMTS/stringmethod/src/data/trajectory_all_25.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/trajectory_all_25.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/trajectory_all_25.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,40 @@
+MODEL 0
+ATOM 1 CA THR A 1 24.572 13.002 -5.044 1.00 1.00 A C
+ATOM 2 CB THR A 2 24.473 11.566 -4.482 1.00 1.00 A C
+ATOM 3 CA TRP A 3 22.518 15.634 -3.182 1.00 1.00 A C
+ATOM 4 CB TRP A 4 21.425 16.539 -3.902 1.00 1.00 A C
+ATOM 5 CA ILE A 5 22.316 14.930 0.518 1.00 1.00 A C
+ATOM 6 CB ILE A 6 23.316 14.040 1.190 1.00 1.00 A C
+ATOM 7 CA GLN A 7 20.540 18.272 1.285 1.00 1.00 A C
+ATOM 8 CB GLN A 8 19.681 19.098 0.293 1.00 1.00 A C
+ATOM 9 CA ASN A 9 20.853 18.805 4.953 1.00 1.00 A C
+ATOM 10 CB ASN A 10 22.179 18.500 5.647 1.00 1.00 A C
+ATOM 11 CA GLY A 11 18.238 21.607 5.519 1.00 1.00 A C
+ATOM 12 CA SER A 12 20.436 24.684 5.432 1.00 1.00 A C
+ATOM 13 CB SER A 13 20.812 25.524 6.545 1.00 1.00 A C
+ATOM 14 CA THR A 14 23.804 22.913 4.867 1.00 1.00 A C
+ATOM 15 CB THR A 15 24.655 22.204 5.943 1.00 1.00 A C
+ATOM 16 CA LYS A 16 23.984 21.758 1.260 1.00 1.00 A C
+ATOM 17 CB LYS A 17 23.779 22.640 0.114 1.00 1.00 A C
+ATOM 18 CA TRP A 18 26.117 18.661 1.404 1.00 1.00 A C
+ATOM 19 CB TRP A 19 26.182 17.743 2.594 1.00 1.00 A C
+ATOM 20 CA TYR A 20 26.485 17.488 -2.177 1.00 1.00 A C
+ATOM 21 CB TYR A 21 26.577 18.464 -3.331 1.00 1.00 A C
+ATOM 22 CA GLN A 22 28.275 14.289 -1.620 1.00 1.00 A C
+ATOM 23 CB GLN A 23 27.763 13.060 -0.889 1.00 1.00 A C
+ATOM 24 CA ASN A 24 31.040 13.578 -4.156 1.00 1.00 A C
+ATOM 25 CB ASN A 25 31.915 14.794 -4.434 1.00 1.00 A C
+ATOM 26 CA GLY A 26 31.814 9.807 -3.587 1.00 1.00 A C
+ATOM 27 CA SER A 27 32.276 10.225 0.180 1.00 1.00 A C
+ATOM 28 CB SER A 28 33.090 9.065 0.874 1.00 1.00 A C
+ATOM 29 CA THR A 29 33.897 13.671 0.660 1.00 1.00 A C
+ATOM 30 CB THR A 30 35.293 14.141 0.218 1.00 1.00 A C
+ATOM 31 CA LYS A 31 30.862 16.111 0.682 1.00 1.00 A C
+ATOM 32 CB LYS A 32 29.946 16.160 1.901 1.00 1.00 A C
+ATOM 33 CA ILE A 33 31.403 19.264 -1.301 1.00 1.00 A C
+ATOM 34 CB ILE A 34 31.850 19.269 -2.807 1.00 1.00 A C
+ATOM 35 CA TYR A 35 29.573 22.401 0.176 1.00 1.00 A C
+ATOM 36 CB TYR A 36 30.087 23.015 1.454 1.00 1.00 A C
+ATOM 37 CA THR A 37 27.180 24.108 -2.122 1.00 1.00 A C
+ATOM 38 CB THR A 38 26.001 23.244 -2.597 1.00 1.00 A C
+ENDMDL
Added: SwiftApps/CMTS/stringmethod/src/data/trajectory_all_26.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/trajectory_all_26.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/trajectory_all_26.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,40 @@
+MODEL 0
+ATOM 1 CA THR A 1 25.019 13.186 -5.011 1.00 1.00 A C
+ATOM 2 CB THR A 2 24.518 11.850 -4.469 1.00 1.00 A C
+ATOM 3 CA TRP A 3 23.011 16.125 -3.456 1.00 1.00 A C
+ATOM 4 CB TRP A 4 21.886 17.021 -4.142 1.00 1.00 A C
+ATOM 5 CA ILE A 5 22.483 15.469 0.301 1.00 1.00 A C
+ATOM 6 CB ILE A 6 23.342 14.700 1.343 1.00 1.00 A C
+ATOM 7 CA GLN A 7 20.537 18.796 0.854 1.00 1.00 A C
+ATOM 8 CB GLN A 8 19.612 19.669 -0.066 1.00 1.00 A C
+ATOM 9 CA ASN A 9 19.974 18.373 4.618 1.00 1.00 A C
+ATOM 10 CB ASN A 10 21.269 17.862 5.375 1.00 1.00 A C
+ATOM 11 CA GLY A 11 17.456 21.239 4.854 1.00 1.00 A C
+ATOM 12 CA SER A 12 19.700 24.127 5.811 1.00 1.00 A C
+ATOM 13 CB SER A 13 19.590 24.555 7.320 1.00 1.00 A C
+ATOM 14 CA THR A 14 23.049 22.422 5.250 1.00 1.00 A C
+ATOM 15 CB THR A 15 23.749 21.471 6.204 1.00 1.00 A C
+ATOM 16 CA LYS A 16 23.702 22.019 1.617 1.00 1.00 A C
+ATOM 17 CB LYS A 17 23.272 23.142 0.642 1.00 1.00 A C
+ATOM 18 CA TRP A 18 26.038 19.010 0.978 1.00 1.00 A C
+ATOM 19 CB TRP A 19 25.992 17.759 1.894 1.00 1.00 A C
+ATOM 20 CA TYR A 20 27.237 17.557 -2.264 1.00 1.00 A C
+ATOM 21 CB TYR A 21 27.483 18.452 -3.451 1.00 1.00 A C
+ATOM 22 CA GLN A 22 28.810 14.118 -2.332 1.00 1.00 A C
+ATOM 23 CB GLN A 23 28.018 12.814 -2.171 1.00 1.00 A C
+ATOM 24 CA ASN A 24 31.616 13.681 -4.723 1.00 1.00 A C
+ATOM 25 CB ASN A 25 32.820 14.627 -4.689 1.00 1.00 A C
+ATOM 26 CA GLY A 26 31.099 10.032 -3.688 1.00 1.00 A C
+ATOM 27 CA SER A 27 32.409 9.978 -0.156 1.00 1.00 A C
+ATOM 28 CB SER A 28 33.371 8.961 0.448 1.00 1.00 A C
+ATOM 29 CA THR A 29 33.850 13.493 -0.017 1.00 1.00 A C
+ATOM 30 CB THR A 30 35.087 13.881 -0.807 1.00 1.00 A C
+ATOM 31 CA LYS A 31 30.953 15.698 1.145 1.00 1.00 A C
+ATOM 32 CB LYS A 32 30.102 15.315 2.363 1.00 1.00 A C
+ATOM 33 CA ILE A 33 31.561 19.175 -0.061 1.00 1.00 A C
+ATOM 34 CB ILE A 34 32.295 19.414 -1.357 1.00 1.00 A C
+ATOM 35 CA TYR A 35 29.577 22.139 1.131 1.00 1.00 A C
+ATOM 36 CB TYR A 36 29.854 22.982 2.323 1.00 1.00 A C
+ATOM 37 CA THR A 37 27.770 23.785 -1.691 1.00 1.00 A C
+ATOM 38 CB THR A 38 26.565 23.130 -2.389 1.00 1.00 A C
+ENDMDL
Added: SwiftApps/CMTS/stringmethod/src/data/trajectory_all_27.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/trajectory_all_27.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/trajectory_all_27.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,40 @@
+MODEL 0
+ATOM 1 CA THR A 1 24.555 14.516 -5.709 1.00 1.00 A C
+ATOM 2 CB THR A 2 23.313 13.745 -6.010 1.00 1.00 A C
+ATOM 3 CA TRP A 3 23.171 17.066 -3.075 1.00 1.00 A C
+ATOM 4 CB TRP A 4 22.331 18.296 -3.382 1.00 1.00 A C
+ATOM 5 CA ILE A 5 22.650 15.559 0.322 1.00 1.00 A C
+ATOM 6 CB ILE A 6 23.791 14.765 1.111 1.00 1.00 A C
+ATOM 7 CA GLN A 7 20.074 17.910 1.700 1.00 1.00 A C
+ATOM 8 CB GLN A 8 18.911 18.486 0.993 1.00 1.00 A C
+ATOM 9 CA ASN A 9 20.132 17.413 5.521 1.00 1.00 A C
+ATOM 10 CB ASN A 10 21.398 17.379 6.451 1.00 1.00 A C
+ATOM 11 CA GLY A 11 16.992 19.515 6.313 1.00 1.00 A C
+ATOM 12 CA SER A 12 17.986 22.879 4.778 1.00 1.00 A C
+ATOM 13 CB SER A 13 17.269 24.251 5.280 1.00 1.00 A C
+ATOM 14 CA THR A 14 21.695 22.161 4.274 1.00 1.00 A C
+ATOM 15 CB THR A 15 22.540 21.995 5.571 1.00 1.00 A C
+ATOM 16 CA LYS A 16 23.446 21.047 0.928 1.00 1.00 A C
+ATOM 17 CB LYS A 17 23.167 21.783 -0.384 1.00 1.00 A C
+ATOM 18 CA TRP A 18 26.356 18.741 1.240 1.00 1.00 A C
+ATOM 19 CB TRP A 19 26.658 17.611 2.281 1.00 1.00 A C
+ATOM 20 CA TYR A 20 27.385 18.015 -2.253 1.00 1.00 A C
+ATOM 21 CB TYR A 21 27.781 19.078 -3.284 1.00 1.00 A C
+ATOM 22 CA GLN A 22 28.445 14.316 -2.320 1.00 1.00 A C
+ATOM 23 CB GLN A 23 27.498 13.252 -1.824 1.00 1.00 A C
+ATOM 24 CA ASN A 24 31.180 13.757 -4.849 1.00 1.00 A C
+ATOM 25 CB ASN A 25 32.246 14.797 -4.989 1.00 1.00 A C
+ATOM 26 CA GLY A 26 31.826 10.019 -4.374 1.00 1.00 A C
+ATOM 27 CA SER A 27 32.397 9.817 -0.563 1.00 1.00 A C
+ATOM 28 CB SER A 28 33.091 8.626 0.072 1.00 1.00 A C
+ATOM 29 CA THR A 29 33.487 13.483 0.168 1.00 1.00 A C
+ATOM 30 CB THR A 30 34.841 14.033 -0.212 1.00 1.00 A C
+ATOM 31 CA LYS A 31 30.762 15.797 1.287 1.00 1.00 A C
+ATOM 32 CB LYS A 32 29.813 15.487 2.414 1.00 1.00 A C
+ATOM 33 CA ILE A 33 32.087 19.216 0.142 1.00 1.00 A C
+ATOM 34 CB ILE A 34 32.721 19.617 -1.197 1.00 1.00 A C
+ATOM 35 CA TYR A 35 30.427 22.313 1.648 1.00 1.00 A C
+ATOM 36 CB TYR A 36 30.937 23.200 2.782 1.00 1.00 A C
+ATOM 37 CA THR A 37 28.247 23.779 -1.096 1.00 1.00 A C
+ATOM 38 CB THR A 38 27.779 22.734 -2.093 1.00 1.00 A C
+ENDMDL
Added: SwiftApps/CMTS/stringmethod/src/data/trajectory_all_28.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/trajectory_all_28.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/trajectory_all_28.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,40 @@
+MODEL 0
+ATOM 1 CA THR A 1 24.207 13.761 -5.087 1.00 1.00 A C
+ATOM 2 CB THR A 2 25.609 13.224 -5.098 1.00 1.00 A C
+ATOM 3 CA TRP A 3 22.516 16.479 -3.055 1.00 1.00 A C
+ATOM 4 CB TRP A 4 21.955 17.706 -3.826 1.00 1.00 A C
+ATOM 5 CA ILE A 5 21.665 15.565 0.405 1.00 1.00 A C
+ATOM 6 CB ILE A 6 22.546 14.545 1.080 1.00 1.00 A C
+ATOM 7 CA GLN A 7 20.032 18.726 1.836 1.00 1.00 A C
+ATOM 8 CB GLN A 8 19.255 19.653 0.944 1.00 1.00 A C
+ATOM 9 CA ASN A 9 19.214 18.006 5.627 1.00 1.00 A C
+ATOM 10 CB ASN A 10 20.133 16.980 6.494 1.00 1.00 A C
+ATOM 11 CA GLY A 11 17.950 21.363 6.836 1.00 1.00 A C
+ATOM 12 CA SER A 12 20.399 23.950 5.825 1.00 1.00 A C
+ATOM 13 CB SER A 13 20.845 25.150 6.757 1.00 1.00 A C
+ATOM 14 CA THR A 14 23.663 22.174 4.972 1.00 1.00 A C
+ATOM 15 CB THR A 15 24.622 21.505 6.130 1.00 1.00 A C
+ATOM 16 CA LYS A 16 23.783 21.255 1.352 1.00 1.00 A C
+ATOM 17 CB LYS A 17 23.406 22.396 0.406 1.00 1.00 A C
+ATOM 18 CA TRP A 18 25.873 18.151 0.985 1.00 1.00 A C
+ATOM 19 CB TRP A 19 25.655 16.903 1.813 1.00 1.00 A C
+ATOM 20 CA TYR A 20 27.139 17.405 -2.572 1.00 1.00 A C
+ATOM 21 CB TYR A 21 27.628 18.375 -3.633 1.00 1.00 A C
+ATOM 22 CA GLN A 22 28.743 14.080 -2.492 1.00 1.00 A C
+ATOM 23 CB GLN A 23 28.061 12.712 -2.312 1.00 1.00 A C
+ATOM 24 CA ASN A 24 31.585 14.973 -4.987 1.00 1.00 A C
+ATOM 25 CB ASN A 25 32.406 16.238 -5.015 1.00 1.00 A C
+ATOM 26 CA GLY A 26 32.779 11.495 -5.623 1.00 1.00 A C
+ATOM 27 CA SER A 27 32.893 10.360 -2.021 1.00 1.00 A C
+ATOM 28 CB SER A 28 33.852 9.197 -1.798 1.00 1.00 A C
+ATOM 29 CA THR A 29 33.711 13.221 0.115 1.00 1.00 A C
+ATOM 30 CB THR A 30 35.111 13.870 -0.125 1.00 1.00 A C
+ATOM 31 CA LYS A 31 30.519 14.785 1.162 1.00 1.00 A C
+ATOM 32 CB LYS A 32 29.632 14.117 2.154 1.00 1.00 A C
+ATOM 33 CA ILE A 33 31.062 18.544 0.991 1.00 1.00 A C
+ATOM 34 CB ILE A 34 32.283 18.965 0.126 1.00 1.00 A C
+ATOM 35 CA TYR A 35 29.218 21.760 1.843 1.00 1.00 A C
+ATOM 36 CB TYR A 36 29.432 22.440 3.243 1.00 1.00 A C
+ATOM 37 CA THR A 37 28.114 23.447 -1.419 1.00 1.00 A C
+ATOM 38 CB THR A 38 27.509 22.670 -2.642 1.00 1.00 A C
+ENDMDL
Added: SwiftApps/CMTS/stringmethod/src/data/trajectory_all_29.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/trajectory_all_29.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/trajectory_all_29.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,40 @@
+MODEL 0
+ATOM 1 CA THR A 1 24.174 13.449 -5.263 1.00 1.00 A C
+ATOM 2 CB THR A 2 23.780 12.075 -4.769 1.00 1.00 A C
+ATOM 3 CA TRP A 3 22.310 16.019 -3.247 1.00 1.00 A C
+ATOM 4 CB TRP A 4 21.310 17.090 -3.884 1.00 1.00 A C
+ATOM 5 CA ILE A 5 22.355 15.309 0.557 1.00 1.00 A C
+ATOM 6 CB ILE A 6 23.402 14.515 1.435 1.00 1.00 A C
+ATOM 7 CA GLN A 7 20.318 17.917 2.075 1.00 1.00 A C
+ATOM 8 CB GLN A 8 18.869 18.044 1.550 1.00 1.00 A C
+ATOM 9 CA ASN A 9 21.637 18.647 5.559 1.00 1.00 A C
+ATOM 10 CB ASN A 10 23.167 18.481 5.989 1.00 1.00 A C
+ATOM 11 CA GLY A 11 18.650 20.228 7.265 1.00 1.00 A C
+ATOM 12 CA SER A 12 18.264 22.936 4.456 1.00 1.00 A C
+ATOM 13 CB SER A 13 17.817 24.199 5.046 1.00 1.00 A C
+ATOM 14 CA THR A 14 21.472 23.471 2.314 1.00 1.00 A C
+ATOM 15 CB THR A 15 22.782 24.246 2.668 1.00 1.00 A C
+ATOM 16 CA LYS A 16 22.273 20.938 -0.406 1.00 1.00 A C
+ATOM 17 CB LYS A 17 21.331 20.979 -1.742 1.00 1.00 A C
+ATOM 18 CA TRP A 18 25.721 19.764 0.251 1.00 1.00 A C
+ATOM 19 CB TRP A 19 26.344 19.582 1.630 1.00 1.00 A C
+ATOM 20 CA TYR A 20 27.057 18.064 -2.762 1.00 1.00 A C
+ATOM 21 CB TYR A 21 27.490 18.817 -4.069 1.00 1.00 A C
+ATOM 22 CA GLN A 22 28.201 14.438 -2.128 1.00 1.00 A C
+ATOM 23 CB GLN A 23 27.258 13.459 -1.489 1.00 1.00 A C
+ATOM 24 CA ASN A 24 30.923 13.942 -4.798 1.00 1.00 A C
+ATOM 25 CB ASN A 25 31.722 15.122 -5.351 1.00 1.00 A C
+ATOM 26 CA GLY A 26 31.172 10.315 -5.043 1.00 1.00 A C
+ATOM 27 CA SER A 27 31.962 9.853 -1.396 1.00 1.00 A C
+ATOM 28 CB SER A 28 33.034 8.767 -0.956 1.00 1.00 A C
+ATOM 29 CA THR A 29 33.102 13.334 -0.312 1.00 1.00 A C
+ATOM 30 CB THR A 30 34.539 13.861 -0.491 1.00 1.00 A C
+ATOM 31 CA LYS A 31 30.808 16.011 1.016 1.00 1.00 A C
+ATOM 32 CB LYS A 32 30.048 15.902 2.325 1.00 1.00 A C
+ATOM 33 CA ILE A 33 32.068 19.410 -0.005 1.00 1.00 A C
+ATOM 34 CB ILE A 34 32.339 19.855 -1.459 1.00 1.00 A C
+ATOM 35 CA TYR A 35 31.835 21.896 2.934 1.00 1.00 A C
+ATOM 36 CB TYR A 36 31.968 21.343 4.346 1.00 1.00 A C
+ATOM 37 CA THR A 37 32.246 25.533 3.644 1.00 1.00 A C
+ATOM 38 CB THR A 38 31.175 26.579 3.225 1.00 1.00 A C
+ENDMDL
Added: SwiftApps/CMTS/stringmethod/src/data/trajectory_all_3.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/trajectory_all_3.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/trajectory_all_3.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,40 @@
+MODEL 0
+ATOM 1 CA THR A 1 24.509 14.166 -4.920 1.00 1.00 A C
+ATOM 2 CB THR A 2 24.176 12.721 -4.405 1.00 1.00 A C
+ATOM 3 CA TRP A 3 23.078 17.478 -3.578 1.00 1.00 A C
+ATOM 4 CB TRP A 4 22.670 18.596 -4.576 1.00 1.00 A C
+ATOM 5 CA ILE A 5 21.301 16.616 -0.282 1.00 1.00 A C
+ATOM 6 CB ILE A 6 21.879 15.610 0.718 1.00 1.00 A C
+ATOM 7 CA GLN A 7 19.076 19.523 0.855 1.00 1.00 A C
+ATOM 8 CB GLN A 8 18.154 20.313 -0.059 1.00 1.00 A C
+ATOM 9 CA ASN A 9 17.626 19.836 4.335 1.00 1.00 A C
+ATOM 10 CB ASN A 10 18.347 19.101 5.419 1.00 1.00 A C
+ATOM 11 CA GLY A 11 15.313 22.718 4.099 1.00 1.00 A C
+ATOM 12 CA SER A 12 18.087 25.363 3.755 1.00 1.00 A C
+ATOM 13 CB SER A 13 17.876 26.650 4.516 1.00 1.00 A C
+ATOM 14 CA THR A 14 21.252 23.410 4.694 1.00 1.00 A C
+ATOM 15 CB THR A 15 21.538 22.650 5.914 1.00 1.00 A C
+ATOM 16 CA LYS A 16 23.113 21.649 1.888 1.00 1.00 A C
+ATOM 17 CB LYS A 17 23.053 22.477 0.567 1.00 1.00 A C
+ATOM 18 CA TRP A 18 25.888 19.200 1.199 1.00 1.00 A C
+ATOM 19 CB TRP A 19 26.319 18.412 2.482 1.00 1.00 A C
+ATOM 20 CA TYR A 20 27.444 17.516 -1.902 1.00 1.00 A C
+ATOM 21 CB TYR A 21 28.083 18.444 -2.900 1.00 1.00 A C
+ATOM 22 CA GLN A 22 28.305 13.984 -1.196 1.00 1.00 A C
+ATOM 23 CB GLN A 23 27.169 13.040 -0.930 1.00 1.00 A C
+ATOM 24 CA ASN A 24 31.434 13.220 -2.888 1.00 1.00 A C
+ATOM 25 CB ASN A 25 32.146 14.461 -3.318 1.00 1.00 A C
+ATOM 26 CA GLY A 26 33.190 9.944 -2.608 1.00 1.00 A C
+ATOM 27 CA SER A 27 32.328 9.473 1.051 1.00 1.00 A C
+ATOM 28 CB SER A 28 32.974 8.239 1.615 1.00 1.00 A C
+ATOM 29 CA THR A 29 33.877 11.973 3.551 1.00 1.00 A C
+ATOM 30 CB THR A 30 35.123 11.569 4.435 1.00 1.00 A C
+ATOM 31 CA LYS A 31 34.292 14.764 0.954 1.00 1.00 A C
+ATOM 32 CB LYS A 32 34.991 14.645 -0.348 1.00 1.00 A C
+ATOM 33 CA ILE A 33 31.507 17.086 1.720 1.00 1.00 A C
+ATOM 34 CB ILE A 34 31.043 17.204 3.226 1.00 1.00 A C
+ATOM 35 CA TYR A 35 31.041 20.138 -0.512 1.00 1.00 A C
+ATOM 36 CB TYR A 36 31.438 20.003 -2.040 1.00 1.00 A C
+ATOM 37 CA THR A 37 28.639 23.120 -0.025 1.00 1.00 A C
+ATOM 38 CB THR A 38 29.106 24.354 0.821 1.00 1.00 A C
+ENDMDL
Added: SwiftApps/CMTS/stringmethod/src/data/trajectory_all_30.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/trajectory_all_30.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/trajectory_all_30.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,40 @@
+MODEL 0
+ATOM 1 CA THR A 1 24.242 15.123 -6.583 1.00 1.00 A C
+ATOM 2 CB THR A 2 23.572 13.769 -6.519 1.00 1.00 A C
+ATOM 3 CA TRP A 3 23.126 17.647 -4.049 1.00 1.00 A C
+ATOM 4 CB TRP A 4 22.827 19.060 -4.398 1.00 1.00 A C
+ATOM 5 CA ILE A 5 21.682 16.066 -0.906 1.00 1.00 A C
+ATOM 6 CB ILE A 6 22.296 14.710 -0.496 1.00 1.00 A C
+ATOM 7 CA GLN A 7 20.084 18.106 1.915 1.00 1.00 A C
+ATOM 8 CB GLN A 8 18.695 18.623 1.976 1.00 1.00 A C
+ATOM 9 CA ASN A 9 21.516 17.264 5.428 1.00 1.00 A C
+ATOM 10 CB ASN A 10 22.741 16.453 5.402 1.00 1.00 A C
+ATOM 11 CA GLY A 11 20.933 19.637 8.231 1.00 1.00 A C
+ATOM 12 CA SER A 12 20.613 23.146 6.613 1.00 1.00 A C
+ATOM 13 CB SER A 13 21.761 23.955 7.176 1.00 1.00 A C
+ATOM 14 CA THR A 14 21.517 23.346 2.854 1.00 1.00 A C
+ATOM 15 CB THR A 15 22.355 24.570 2.528 1.00 1.00 A C
+ATOM 16 CA LYS A 16 22.391 20.888 0.071 1.00 1.00 A C
+ATOM 17 CB LYS A 17 21.918 20.817 -1.371 1.00 1.00 A C
+ATOM 18 CA TRP A 18 25.787 19.528 0.173 1.00 1.00 A C
+ATOM 19 CB TRP A 19 26.507 18.992 1.479 1.00 1.00 A C
+ATOM 20 CA TYR A 20 27.392 17.861 -2.782 1.00 1.00 A C
+ATOM 21 CB TYR A 21 28.234 18.751 -3.819 1.00 1.00 A C
+ATOM 22 CA GLN A 22 27.936 14.222 -2.463 1.00 1.00 A C
+ATOM 23 CB GLN A 23 26.704 13.322 -2.470 1.00 1.00 A C
+ATOM 24 CA ASN A 24 31.341 13.404 -3.936 1.00 1.00 A C
+ATOM 25 CB ASN A 25 32.309 14.505 -4.281 1.00 1.00 A C
+ATOM 26 CA GLY A 26 31.308 9.709 -3.109 1.00 1.00 A C
+ATOM 27 CA SER A 27 32.163 9.761 0.667 1.00 1.00 A C
+ATOM 28 CB SER A 28 33.482 9.239 1.273 1.00 1.00 A C
+ATOM 29 CA THR A 29 32.888 13.419 1.328 1.00 1.00 A C
+ATOM 30 CB THR A 30 34.211 14.017 0.898 1.00 1.00 A C
+ATOM 31 CA LYS A 31 30.233 16.085 1.266 1.00 1.00 A C
+ATOM 32 CB LYS A 32 29.058 16.286 2.276 1.00 1.00 A C
+ATOM 33 CA ILE A 33 31.446 18.988 -0.629 1.00 1.00 A C
+ATOM 34 CB ILE A 34 31.732 19.069 -2.146 1.00 1.00 A C
+ATOM 35 CA TYR A 35 29.934 21.799 1.390 1.00 1.00 A C
+ATOM 36 CB TYR A 36 30.474 22.200 2.791 1.00 1.00 A C
+ATOM 37 CA THR A 37 28.276 24.393 -1.043 1.00 1.00 A C
+ATOM 38 CB THR A 38 26.795 24.484 -1.353 1.00 1.00 A C
+ENDMDL
Added: SwiftApps/CMTS/stringmethod/src/data/trajectory_all_31.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/trajectory_all_31.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/trajectory_all_31.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,40 @@
+MODEL 0
+ATOM 1 CA THR A 1 24.970 13.268 -5.417 1.00 1.00 A C
+ATOM 2 CB THR A 2 24.958 11.988 -4.488 1.00 1.00 A C
+ATOM 3 CA TRP A 3 23.288 16.402 -4.056 1.00 1.00 A C
+ATOM 4 CB TRP A 4 22.758 17.623 -4.796 1.00 1.00 A C
+ATOM 5 CA ILE A 5 21.657 15.735 -0.612 1.00 1.00 A C
+ATOM 6 CB ILE A 6 22.241 14.800 0.423 1.00 1.00 A C
+ATOM 7 CA GLN A 7 19.362 18.487 0.537 1.00 1.00 A C
+ATOM 8 CB GLN A 8 18.259 18.834 -0.402 1.00 1.00 A C
+ATOM 9 CA ASN A 9 19.144 18.356 4.364 1.00 1.00 A C
+ATOM 10 CB ASN A 10 20.155 17.689 5.269 1.00 1.00 A C
+ATOM 11 CA GLY A 11 17.210 21.531 4.872 1.00 1.00 A C
+ATOM 12 CA SER A 12 19.783 24.421 4.998 1.00 1.00 A C
+ATOM 13 CB SER A 13 19.759 25.500 6.043 1.00 1.00 A C
+ATOM 14 CA THR A 14 22.769 22.072 5.026 1.00 1.00 A C
+ATOM 15 CB THR A 15 23.339 21.284 6.136 1.00 1.00 A C
+ATOM 16 CA LYS A 16 23.243 21.634 1.271 1.00 1.00 A C
+ATOM 17 CB LYS A 17 22.882 22.612 0.259 1.00 1.00 A C
+ATOM 18 CA TRP A 18 25.808 18.848 0.383 1.00 1.00 A C
+ATOM 19 CB TRP A 19 25.929 17.791 1.524 1.00 1.00 A C
+ATOM 20 CA TYR A 20 27.359 17.883 -2.804 1.00 1.00 A C
+ATOM 21 CB TYR A 21 28.001 18.714 -3.800 1.00 1.00 A C
+ATOM 22 CA GLN A 22 28.609 14.455 -1.949 1.00 1.00 A C
+ATOM 23 CB GLN A 23 27.869 13.494 -1.080 1.00 1.00 A C
+ATOM 24 CA ASN A 24 31.043 13.342 -4.609 1.00 1.00 A C
+ATOM 25 CB ASN A 25 32.077 14.353 -5.042 1.00 1.00 A C
+ATOM 26 CA GLY A 26 31.123 9.761 -3.209 1.00 1.00 A C
+ATOM 27 CA SER A 27 32.993 10.346 -0.004 1.00 1.00 A C
+ATOM 28 CB SER A 28 34.080 9.452 0.216 1.00 1.00 A C
+ATOM 29 CA THR A 29 33.964 14.041 -0.444 1.00 1.00 A C
+ATOM 30 CB THR A 30 35.026 14.407 -1.403 1.00 1.00 A C
+ATOM 31 CA LYS A 31 31.355 16.403 1.001 1.00 1.00 A C
+ATOM 32 CB LYS A 32 31.029 16.041 2.519 1.00 1.00 A C
+ATOM 33 CA ILE A 33 31.209 19.890 -0.638 1.00 1.00 A C
+ATOM 34 CB ILE A 34 31.401 19.946 -2.164 1.00 1.00 A C
+ATOM 35 CA TYR A 35 29.567 22.455 1.634 1.00 1.00 A C
+ATOM 36 CB TYR A 36 30.247 22.998 2.943 1.00 1.00 A C
+ATOM 37 CA THR A 37 27.508 24.566 -0.592 1.00 1.00 A C
+ATOM 38 CB THR A 38 26.681 24.014 -1.905 1.00 1.00 A C
+ENDMDL
Added: SwiftApps/CMTS/stringmethod/src/data/trajectory_all_4.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/trajectory_all_4.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/trajectory_all_4.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,40 @@
+MODEL 0
+ATOM 1 CA THR A 1 25.693 13.770 -4.875 1.00 1.00 A C
+ATOM 2 CB THR A 2 25.330 12.805 -3.761 1.00 1.00 A C
+ATOM 3 CA TRP A 3 23.228 16.580 -4.231 1.00 1.00 A C
+ATOM 4 CB TRP A 4 22.463 17.226 -5.337 1.00 1.00 A C
+ATOM 5 CA ILE A 5 22.236 16.463 -0.650 1.00 1.00 A C
+ATOM 6 CB ILE A 6 23.423 15.782 0.110 1.00 1.00 A C
+ATOM 7 CA GLN A 7 19.794 18.333 1.448 1.00 1.00 A C
+ATOM 8 CB GLN A 8 18.580 18.892 0.719 1.00 1.00 A C
+ATOM 9 CA ASN A 9 19.049 18.009 5.136 1.00 1.00 A C
+ATOM 10 CB ASN A 10 20.032 17.682 6.239 1.00 1.00 A C
+ATOM 11 CA GLY A 11 16.419 20.659 6.079 1.00 1.00 A C
+ATOM 12 CA SER A 12 16.240 23.900 4.201 1.00 1.00 A C
+ATOM 13 CB SER A 13 15.738 25.258 4.740 1.00 1.00 A C
+ATOM 14 CA THR A 14 19.828 24.062 3.008 1.00 1.00 A C
+ATOM 15 CB THR A 15 20.840 24.302 4.157 1.00 1.00 A C
+ATOM 16 CA LYS A 16 21.369 22.723 -0.153 1.00 1.00 A C
+ATOM 17 CB LYS A 17 20.907 23.280 -1.569 1.00 1.00 A C
+ATOM 18 CA TRP A 18 25.028 21.733 -0.048 1.00 1.00 A C
+ATOM 19 CB TRP A 19 25.656 21.808 1.338 1.00 1.00 A C
+ATOM 20 CA TYR A 20 27.079 19.324 -2.216 1.00 1.00 A C
+ATOM 21 CB TYR A 21 27.736 20.058 -3.403 1.00 1.00 A C
+ATOM 22 CA GLN A 22 28.731 15.977 -1.474 1.00 1.00 A C
+ATOM 23 CB GLN A 23 27.832 15.001 -0.722 1.00 1.00 A C
+ATOM 24 CA ASN A 24 31.767 14.428 -3.209 1.00 1.00 A C
+ATOM 25 CB ASN A 25 33.255 14.701 -2.895 1.00 1.00 A C
+ATOM 26 CA GLY A 26 30.007 11.198 -3.651 1.00 1.00 A C
+ATOM 27 CA SER A 27 29.241 9.859 -0.240 1.00 1.00 A C
+ATOM 28 CB SER A 28 28.834 8.388 -0.128 1.00 1.00 A C
+ATOM 29 CA THR A 29 32.514 11.279 1.300 1.00 1.00 A C
+ATOM 30 CB THR A 30 33.800 10.684 0.638 1.00 1.00 A C
+ATOM 31 CA LYS A 31 33.671 14.853 1.409 1.00 1.00 A C
+ATOM 32 CB LYS A 32 34.969 15.341 0.833 1.00 1.00 A C
+ATOM 33 CA ILE A 33 31.276 17.586 2.246 1.00 1.00 A C
+ATOM 34 CB ILE A 34 30.884 17.686 3.764 1.00 1.00 A C
+ATOM 35 CA TYR A 35 31.304 20.869 0.273 1.00 1.00 A C
+ATOM 36 CB TYR A 36 31.470 20.868 -1.244 1.00 1.00 A C
+ATOM 37 CA THR A 37 29.466 23.386 2.612 1.00 1.00 A C
+ATOM 38 CB THR A 38 29.671 23.366 4.159 1.00 1.00 A C
+ENDMDL
Added: SwiftApps/CMTS/stringmethod/src/data/trajectory_all_5.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/trajectory_all_5.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/trajectory_all_5.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,40 @@
+MODEL 0
+ATOM 1 CA THR A 1 24.354 13.682 -3.743 1.00 1.00 A C
+ATOM 2 CB THR A 2 24.072 13.205 -5.190 1.00 1.00 A C
+ATOM 3 CA TRP A 3 23.172 17.338 -4.179 1.00 1.00 A C
+ATOM 4 CB TRP A 4 22.810 18.034 -5.436 1.00 1.00 A C
+ATOM 5 CA ILE A 5 21.997 16.774 -0.851 1.00 1.00 A C
+ATOM 6 CB ILE A 6 22.833 15.760 0.008 1.00 1.00 A C
+ATOM 7 CA GLN A 7 19.412 18.905 0.748 1.00 1.00 A C
+ATOM 8 CB GLN A 8 18.166 19.300 0.064 1.00 1.00 A C
+ATOM 9 CA ASN A 9 19.214 18.564 4.550 1.00 1.00 A C
+ATOM 10 CB ASN A 10 20.432 17.969 5.372 1.00 1.00 A C
+ATOM 11 CA GLY A 11 15.997 20.100 5.704 1.00 1.00 A C
+ATOM 12 CA SER A 12 16.517 23.713 4.908 1.00 1.00 A C
+ATOM 13 CB SER A 13 16.459 24.770 6.091 1.00 1.00 A C
+ATOM 14 CA THR A 14 20.118 23.883 3.679 1.00 1.00 A C
+ATOM 15 CB THR A 15 21.245 23.867 4.810 1.00 1.00 A C
+ATOM 16 CA LYS A 16 21.506 22.283 0.476 1.00 1.00 A C
+ATOM 17 CB LYS A 17 20.692 22.713 -0.747 1.00 1.00 A C
+ATOM 18 CA TRP A 18 25.006 21.015 -0.140 1.00 1.00 A C
+ATOM 19 CB TRP A 19 25.895 21.006 1.195 1.00 1.00 A C
+ATOM 20 CA TYR A 20 26.847 18.360 -2.163 1.00 1.00 A C
+ATOM 21 CB TYR A 21 27.707 19.000 -3.266 1.00 1.00 A C
+ATOM 22 CA GLN A 22 28.389 14.919 -1.138 1.00 1.00 A C
+ATOM 23 CB GLN A 23 27.491 13.938 -0.497 1.00 1.00 A C
+ATOM 24 CA ASN A 24 31.130 13.502 -3.394 1.00 1.00 A C
+ATOM 25 CB ASN A 25 32.044 14.486 -4.027 1.00 1.00 A C
+ATOM 26 CA GLY A 26 32.022 9.924 -2.756 1.00 1.00 A C
+ATOM 27 CA SER A 27 31.032 9.386 0.897 1.00 1.00 A C
+ATOM 28 CB SER A 28 30.959 7.920 1.272 1.00 1.00 A C
+ATOM 29 CA THR A 29 33.762 11.643 2.218 1.00 1.00 A C
+ATOM 30 CB THR A 30 35.062 11.093 1.631 1.00 1.00 A C
+ATOM 31 CA LYS A 31 33.747 15.072 0.560 1.00 1.00 A C
+ATOM 32 CB LYS A 32 34.393 15.360 -0.807 1.00 1.00 A C
+ATOM 33 CA ILE A 33 31.016 17.265 2.143 1.00 1.00 A C
+ATOM 34 CB ILE A 34 30.661 17.551 3.576 1.00 1.00 A C
+ATOM 35 CA TYR A 35 31.076 20.325 -0.073 1.00 1.00 A C
+ATOM 36 CB TYR A 36 30.987 20.117 -1.548 1.00 1.00 A C
+ATOM 37 CA THR A 37 29.459 23.465 1.648 1.00 1.00 A C
+ATOM 38 CB THR A 38 29.129 23.573 3.139 1.00 1.00 A C
+ENDMDL
Added: SwiftApps/CMTS/stringmethod/src/data/trajectory_all_6.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/trajectory_all_6.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/trajectory_all_6.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,40 @@
+MODEL 0
+ATOM 1 CA THR A 1 24.295 12.856 -5.265 1.00 1.00 A C
+ATOM 2 CB THR A 2 23.959 11.629 -4.376 1.00 1.00 A C
+ATOM 3 CA TRP A 3 22.392 15.654 -3.421 1.00 1.00 A C
+ATOM 4 CB TRP A 4 20.817 15.976 -3.668 1.00 1.00 A C
+ATOM 5 CA ILE A 5 23.452 16.562 0.099 1.00 1.00 A C
+ATOM 6 CB ILE A 6 25.034 16.498 0.470 1.00 1.00 A C
+ATOM 7 CA GLN A 7 21.517 18.878 2.265 1.00 1.00 A C
+ATOM 8 CB GLN A 8 20.051 18.385 2.496 1.00 1.00 A C
+ATOM 9 CA ASN A 9 22.809 21.068 5.176 1.00 1.00 A C
+ATOM 10 CB ASN A 10 24.348 21.133 5.184 1.00 1.00 A C
+ATOM 11 CA GLY A 11 20.450 23.452 7.208 1.00 1.00 A C
+ATOM 12 CA SER A 12 18.559 24.798 4.172 1.00 1.00 A C
+ATOM 13 CB SER A 13 17.974 26.179 4.318 1.00 1.00 A C
+ATOM 14 CA THR A 14 20.909 24.370 1.224 1.00 1.00 A C
+ATOM 15 CB THR A 15 22.313 25.098 1.232 1.00 1.00 A C
+ATOM 16 CA LYS A 16 20.572 21.559 -1.095 1.00 1.00 A C
+ATOM 17 CB LYS A 17 19.125 21.066 -1.296 1.00 1.00 A C
+ATOM 18 CA TRP A 18 23.657 20.909 -3.261 1.00 1.00 A C
+ATOM 19 CB TRP A 19 24.849 21.953 -3.032 1.00 1.00 A C
+ATOM 20 CA TYR A 20 24.662 17.909 -5.582 1.00 1.00 A C
+ATOM 21 CB TYR A 21 24.186 17.697 -7.044 1.00 1.00 A C
+ATOM 22 CA GLN A 22 28.152 16.811 -5.103 1.00 1.00 A C
+ATOM 23 CB GLN A 23 28.894 17.540 -3.925 1.00 1.00 A C
+ATOM 24 CA ASN A 24 29.675 13.411 -5.899 1.00 1.00 A C
+ATOM 25 CB ASN A 25 29.064 12.756 -7.091 1.00 1.00 A C
+ATOM 26 CA GLY A 26 32.999 11.817 -5.333 1.00 1.00 A C
+ATOM 27 CA SER A 27 34.631 14.632 -3.252 1.00 1.00 A C
+ATOM 28 CB SER A 28 35.250 15.871 -3.947 1.00 1.00 A C
+ATOM 29 CA THR A 29 32.267 14.243 -0.281 1.00 1.00 A C
+ATOM 30 CB THR A 30 30.949 13.349 -0.415 1.00 1.00 A C
+ATOM 31 CA LYS A 31 33.952 15.213 2.849 1.00 1.00 A C
+ATOM 32 CB LYS A 32 34.876 16.398 2.956 1.00 1.00 A C
+ATOM 33 CA ILE A 33 32.455 15.355 6.296 1.00 1.00 A C
+ATOM 34 CB ILE A 34 32.874 14.772 7.600 1.00 1.00 A C
+ATOM 35 CA TYR A 35 29.750 18.082 6.415 1.00 1.00 A C
+ATOM 36 CB TYR A 36 28.859 18.476 5.202 1.00 1.00 A C
+ATOM 37 CA THR A 37 28.878 19.290 9.873 1.00 1.00 A C
+ATOM 38 CB THR A 38 29.776 19.699 11.036 1.00 1.00 A C
+ENDMDL
Added: SwiftApps/CMTS/stringmethod/src/data/trajectory_all_7.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/trajectory_all_7.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/trajectory_all_7.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,40 @@
+MODEL 0
+ATOM 1 CA THR A 1 24.683 12.426 -4.729 1.00 1.00 A C
+ATOM 2 CB THR A 2 25.211 11.344 -3.747 1.00 1.00 A C
+ATOM 3 CA TRP A 3 22.407 15.043 -3.261 1.00 1.00 A C
+ATOM 4 CB TRP A 4 20.990 15.376 -3.761 1.00 1.00 A C
+ATOM 5 CA ILE A 5 23.374 15.762 0.275 1.00 1.00 A C
+ATOM 6 CB ILE A 6 24.806 15.173 0.321 1.00 1.00 A C
+ATOM 7 CA GLN A 7 21.534 17.949 2.629 1.00 1.00 A C
+ATOM 8 CB GLN A 8 20.018 17.622 2.783 1.00 1.00 A C
+ATOM 9 CA ASN A 9 23.302 19.741 5.381 1.00 1.00 A C
+ATOM 10 CB ASN A 10 24.643 20.237 4.936 1.00 1.00 A C
+ATOM 11 CA GLY A 11 20.985 21.660 7.595 1.00 1.00 A C
+ATOM 12 CA SER A 12 18.526 22.931 4.881 1.00 1.00 A C
+ATOM 13 CB SER A 13 17.807 24.243 5.300 1.00 1.00 A C
+ATOM 14 CA THR A 14 20.609 23.136 1.661 1.00 1.00 A C
+ATOM 15 CB THR A 15 21.658 24.238 1.902 1.00 1.00 A C
+ATOM 16 CA LYS A 16 21.132 20.402 -0.997 1.00 1.00 A C
+ATOM 17 CB LYS A 17 19.948 19.899 -1.847 1.00 1.00 A C
+ATOM 18 CA TRP A 18 24.426 20.330 -2.832 1.00 1.00 A C
+ATOM 19 CB TRP A 19 25.783 20.273 -2.073 1.00 1.00 A C
+ATOM 20 CA TYR A 20 25.272 18.270 -5.977 1.00 1.00 A C
+ATOM 21 CB TYR A 21 24.921 18.606 -7.466 1.00 1.00 A C
+ATOM 22 CA GLN A 22 28.346 16.497 -4.993 1.00 1.00 A C
+ATOM 23 CB GLN A 23 28.416 16.303 -3.493 1.00 1.00 A C
+ATOM 24 CA ASN A 24 30.397 13.627 -6.488 1.00 1.00 A C
+ATOM 25 CB ASN A 25 30.741 14.000 -7.946 1.00 1.00 A C
+ATOM 26 CA GLY A 26 32.365 10.905 -4.802 1.00 1.00 A C
+ATOM 27 CA SER A 27 33.678 12.367 -1.567 1.00 1.00 A C
+ATOM 28 CB SER A 28 35.082 12.879 -1.387 1.00 1.00 A C
+ATOM 29 CA THR A 29 30.964 13.580 0.651 1.00 1.00 A C
+ATOM 30 CB THR A 30 29.901 12.666 1.167 1.00 1.00 A C
+ATOM 31 CA LYS A 31 32.099 16.817 2.236 1.00 1.00 A C
+ATOM 32 CB LYS A 32 32.640 17.865 1.220 1.00 1.00 A C
+ATOM 33 CA ILE A 33 30.689 17.558 5.677 1.00 1.00 A C
+ATOM 34 CB ILE A 34 30.745 16.502 6.733 1.00 1.00 A C
+ATOM 35 CA TYR A 35 31.031 21.351 6.250 1.00 1.00 A C
+ATOM 36 CB TYR A 36 30.476 22.412 5.263 1.00 1.00 A C
+ATOM 37 CA THR A 37 30.595 20.819 10.004 1.00 1.00 A C
+ATOM 38 CB THR A 38 31.726 20.066 10.785 1.00 1.00 A C
+ENDMDL
Added: SwiftApps/CMTS/stringmethod/src/data/trajectory_all_8.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/trajectory_all_8.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/trajectory_all_8.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,40 @@
+MODEL 0
+ATOM 1 CA THR A 1 22.519 13.738 -5.798 1.00 1.00 A C
+ATOM 2 CB THR A 2 21.174 13.241 -6.482 1.00 1.00 A C
+ATOM 3 CA TRP A 3 21.680 17.063 -4.195 1.00 1.00 A C
+ATOM 4 CB TRP A 4 21.368 18.254 -5.024 1.00 1.00 A C
+ATOM 5 CA ILE A 5 20.960 15.862 -0.633 1.00 1.00 A C
+ATOM 6 CB ILE A 6 21.593 14.457 -0.239 1.00 1.00 A C
+ATOM 7 CA GLN A 7 19.643 18.019 2.060 1.00 1.00 A C
+ATOM 8 CB GLN A 8 18.166 17.961 2.419 1.00 1.00 A C
+ATOM 9 CA ASN A 9 22.550 18.355 4.583 1.00 1.00 A C
+ATOM 10 CB ASN A 10 23.865 17.956 4.134 1.00 1.00 A C
+ATOM 11 CA GLY A 11 22.112 20.686 7.505 1.00 1.00 A C
+ATOM 12 CA SER A 12 19.647 23.169 6.024 1.00 1.00 A C
+ATOM 13 CB SER A 13 19.774 24.524 6.642 1.00 1.00 A C
+ATOM 14 CA THR A 14 20.956 23.241 2.486 1.00 1.00 A C
+ATOM 15 CB THR A 15 22.162 24.280 2.501 1.00 1.00 A C
+ATOM 16 CA LYS A 16 20.937 21.208 -0.809 1.00 1.00 A C
+ATOM 17 CB LYS A 17 20.166 21.242 -2.198 1.00 1.00 A C
+ATOM 18 CA TRP A 18 24.400 19.717 -1.105 1.00 1.00 A C
+ATOM 19 CB TRP A 19 25.367 19.937 0.060 1.00 1.00 A C
+ATOM 20 CA TYR A 20 25.837 17.159 -3.476 1.00 1.00 A C
+ATOM 21 CB TYR A 21 26.415 17.756 -4.736 1.00 1.00 A C
+ATOM 22 CA GLN A 22 27.076 13.646 -2.810 1.00 1.00 A C
+ATOM 23 CB GLN A 23 26.410 12.822 -1.844 1.00 1.00 A C
+ATOM 24 CA ASN A 24 29.300 12.125 -5.376 1.00 1.00 A C
+ATOM 25 CB ASN A 25 30.226 13.246 -5.961 1.00 1.00 A C
+ATOM 26 CA GLY A 26 31.284 9.550 -3.459 1.00 1.00 A C
+ATOM 27 CA SER A 27 33.886 11.627 -1.711 1.00 1.00 A C
+ATOM 28 CB SER A 28 34.830 12.469 -2.666 1.00 1.00 A C
+ATOM 29 CA THR A 29 34.420 13.346 1.619 1.00 1.00 A C
+ATOM 30 CB THR A 30 35.489 12.945 2.617 1.00 1.00 A C
+ATOM 31 CA LYS A 31 33.324 16.930 1.528 1.00 1.00 A C
+ATOM 32 CB LYS A 32 32.184 17.284 0.663 1.00 1.00 A C
+ATOM 33 CA ILE A 33 33.972 19.666 3.964 1.00 1.00 A C
+ATOM 34 CB ILE A 34 35.096 20.630 3.570 1.00 1.00 A C
+ATOM 35 CA TYR A 35 30.350 20.843 3.722 1.00 1.00 A C
+ATOM 36 CB TYR A 36 29.506 20.855 2.411 1.00 1.00 A C
+ATOM 37 CA THR A 37 28.975 20.298 7.213 1.00 1.00 A C
+ATOM 38 CB THR A 38 29.845 20.363 8.494 1.00 1.00 A C
+ENDMDL
Added: SwiftApps/CMTS/stringmethod/src/data/trajectory_all_9.pdb
===================================================================
--- SwiftApps/CMTS/stringmethod/src/data/trajectory_all_9.pdb (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/data/trajectory_all_9.pdb 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,40 @@
+MODEL 0
+ATOM 1 CA THR A 1 24.035 13.320 -4.882 1.00 1.00 A C
+ATOM 2 CB THR A 2 23.309 12.185 -4.265 1.00 1.00 A C
+ATOM 3 CA TRP A 3 22.354 16.633 -3.898 1.00 1.00 A C
+ATOM 4 CB TRP A 4 21.376 17.407 -4.740 1.00 1.00 A C
+ATOM 5 CA ILE A 5 22.053 16.244 -0.186 1.00 1.00 A C
+ATOM 6 CB ILE A 6 23.183 15.722 0.618 1.00 1.00 A C
+ATOM 7 CA GLN A 7 19.755 18.312 1.908 1.00 1.00 A C
+ATOM 8 CB GLN A 8 18.211 18.194 2.048 1.00 1.00 A C
+ATOM 9 CA ASN A 9 22.029 19.088 4.784 1.00 1.00 A C
+ATOM 10 CB ASN A 10 23.572 19.266 4.496 1.00 1.00 A C
+ATOM 11 CA GLY A 11 19.350 20.889 6.990 1.00 1.00 A C
+ATOM 12 CA SER A 12 18.274 23.699 4.669 1.00 1.00 A C
+ATOM 13 CB SER A 13 17.795 24.944 5.463 1.00 1.00 A C
+ATOM 14 CA THR A 14 21.392 23.683 2.420 1.00 1.00 A C
+ATOM 15 CB THR A 15 22.776 24.183 2.890 1.00 1.00 A C
+ATOM 16 CA LYS A 16 21.388 21.988 -0.938 1.00 1.00 A C
+ATOM 17 CB LYS A 17 20.339 22.299 -2.010 1.00 1.00 A C
+ATOM 18 CA TRP A 18 24.885 20.857 -1.728 1.00 1.00 A C
+ATOM 19 CB TRP A 19 25.856 21.022 -0.532 1.00 1.00 A C
+ATOM 20 CA TYR A 20 26.404 18.311 -4.108 1.00 1.00 A C
+ATOM 21 CB TYR A 21 26.687 18.795 -5.565 1.00 1.00 A C
+ATOM 22 CA GLN A 22 28.370 15.289 -2.981 1.00 1.00 A C
+ATOM 23 CB GLN A 23 27.796 14.175 -2.143 1.00 1.00 A C
+ATOM 24 CA ASN A 24 30.730 13.627 -5.396 1.00 1.00 A C
+ATOM 25 CB ASN A 25 32.281 13.777 -5.460 1.00 1.00 A C
+ATOM 26 CA GLY A 26 29.909 10.201 -4.129 1.00 1.00 A C
+ATOM 27 CA SER A 27 31.606 9.694 -0.709 1.00 1.00 A C
+ATOM 28 CB SER A 28 32.623 8.493 -0.835 1.00 1.00 A C
+ATOM 29 CA THR A 29 33.427 12.862 0.165 1.00 1.00 A C
+ATOM 30 CB THR A 30 34.565 13.323 -0.771 1.00 1.00 A C
+ATOM 31 CA LYS A 31 31.911 15.641 2.314 1.00 1.00 A C
+ATOM 32 CB LYS A 32 31.111 15.428 3.548 1.00 1.00 A C
+ATOM 33 CA ILE A 33 34.066 18.760 2.418 1.00 1.00 A C
+ATOM 34 CB ILE A 34 34.977 18.965 1.092 1.00 1.00 A C
+ATOM 35 CA TYR A 35 31.425 21.293 3.279 1.00 1.00 A C
+ATOM 36 CB TYR A 36 30.009 21.332 2.797 1.00 1.00 A C
+ATOM 37 CA THR A 37 30.831 20.349 7.034 1.00 1.00 A C
+ATOM 38 CB THR A 38 29.489 19.737 7.428 1.00 1.00 A C
+ENDMDL
Added: SwiftApps/CMTS/stringmethod/src/en_boltzmann_mixing_stuff.c
===================================================================
--- SwiftApps/CMTS/stringmethod/src/en_boltzmann_mixing_stuff.c (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/en_boltzmann_mixing_stuff.c 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,1524 @@
+/*Input/Output and other routines related to two state or multistate elastic network based Hamiltonian*/
+
+/*Last modified on December 19, 2011*/
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <time.h>
+#include <string.h>
+
+#include "en_boltzmann_mixing_stuff.h"
+
+/*
+ * Input file name: EN_BOLTZMANN_MIXING_INFO
+ * Format:
+ * NUM_C_ALPHA_ATOMS (%d number of C-alpha atoms)
+ * NUM_INPUT_STRUCTURES (%d number of input structures i.e. number of states)
+ * CUTOFF_DISTANCES (cutoff distances for each structure, separated by white space. Number of cutoffs should be equal
+ * to number of strcutures)
+ * MIXING_COEFFICIENTS (Mixing coeficients for mixing potentials for various structures. Number of coefficients
+ * should be one less than the number of structures. Values should be separated by white space)
+ * SIGMA_REPULSIVE (%lf sigma for the repulsive part of the potential. Same sigma is used for all pairs)
+ * EPSILON_REPULSIVE (%lf epsilon for the repulsive part of the potential)
+ * FIXED_VALUE_OF_FORCE_CONSANT (%lf. Fixed value of force constnat. This value is used unless a different
+ * site dependent value is required to minimize strain. See Albert pan's
+ * string apper JPCB 112, 3432 (2008).)
+ * ENERGY_PARAM_FOR_FORCE_CONSTANT (%lf Energy parameter for site dependent force constant. See the above paper.)
+ * ENERGY_DIFFERENCE_FROM_FIRST_STRUCTURE (%lf Energy difference between the two input structures)
+ * */
+void Read_en_info(int *Num_atoms, int *Num_input_structures, double **aray_of_cutoff_distance, double **array_of_mixing_parameters, double *repulsive_sigma, double *repulsive_epsilon, double *fixed_value_of_force_constant, double *energy_parameter_for_force_constant, double *energy_difference_from_first_structure)
+{
+ FILE *in;
+ char key[1000];
+ int i;
+ in = fopen("EN_BOLTZMANN_MIXING_INFO", "r");
+ if(in == NULL)
+ {
+ printf("File 'EN_BOLTZMANN_MIXING_INFO' not found\n");
+ exit(1);
+ }
+
+ fscanf(in, "%s %d ", key, Num_atoms);
+ fscanf(in, "%s %d ", key, Num_input_structures);
+
+ *aray_of_cutoff_distance = (double*)malloc((*Num_input_structures) * sizeof(double));
+ *array_of_mixing_parameters = (double*)malloc(((*Num_input_structures) - 1) * sizeof(double));
+
+ fscanf(in, "%s ", key);
+ for(i = 0 ; i < *Num_input_structures ; i++)
+ {
+ fscanf(in, " %lf ", &(*aray_of_cutoff_distance)[i]);
+ }
+ fscanf(in, "%s ", key);
+ for(i = 0 ; i < ((*Num_input_structures) - 1) ; i++)
+ {
+ fscanf(in, " %lf ", &(*array_of_mixing_parameters)[i]);
+ }
+
+ fscanf(in, "%s %lf ", key, repulsive_sigma);
+ fscanf(in, "%s %lf ", key, repulsive_epsilon);
+ fscanf(in, "%s %lf ", key, fixed_value_of_force_constant);
+ fscanf(in, "%s %lf ", key, energy_parameter_for_force_constant);
+ fscanf(in, "%s %lf ", key, energy_difference_from_first_structure);
+
+
+ fclose(in);
+
+}
+
+void Read_en_info2(int *Num_atoms, int *Num_input_structures, double **aray_of_cutoff_distance, double **array_of_mixing_parameters, double *repulsive_sigma, double *repulsive_epsilon, double *fixed_value_of_force_constant, double *energy_parameter_for_force_constant, double *energy_difference_from_first_structure)
+{
+ FILE *in;
+ char key[1000];
+ int i;
+ in = fopen("EN_BOLTZMANN_MIXING_INFO_2", "r");
+ if(in == NULL)
+ {
+ printf("File 'EN_BOLTZMANN_MIXING_INFO_2' not found\n");
+ exit(1);
+ }
+
+ fscanf(in, "%s %d ", key, Num_atoms);
+ fscanf(in, "%s %d ", key, Num_input_structures);
+
+ *aray_of_cutoff_distance = (double*)malloc((*Num_input_structures) * sizeof(double));
+ *array_of_mixing_parameters = (double*)malloc(((*Num_input_structures) - 1) * sizeof(double));
+
+ fscanf(in, "%s ", key);
+ for(i = 0 ; i < *Num_input_structures ; i++)
+ {
+ fscanf(in, " %lf ", &(*aray_of_cutoff_distance)[i]);
+ }
+ fscanf(in, "%s ", key);
+ for(i = 0 ; i < ((*Num_input_structures) - 1) ; i++)
+ {
+ fscanf(in, " %lf ", &(*array_of_mixing_parameters)[i]);
+ }
+
+ fscanf(in, "%s %lf ", key, repulsive_sigma);
+ fscanf(in, "%s %lf ", key, repulsive_epsilon);
+ fscanf(in, "%s %lf ", key, fixed_value_of_force_constant);
+ fscanf(in, "%s %lf ", key, energy_parameter_for_force_constant);
+ fscanf(in, "%s %lf ", key, energy_difference_from_first_structure);
+
+
+ fclose(in);
+
+}
+
+
+/*for testing*/
+void Print_en_input(int Num_atoms, int Num_input_structures, double *aray_of_cutoff_distance, double *array_of_mixing_parameters, double repulsive_sigma, double repulsive_epsilon, double fixed_value_of_force_constant, double energy_parameter_for_force_constant, double energy_difference_from_first_structure)
+{
+ FILE *out;
+ int i;
+
+ out = fopen("out_en_boltzmann_mixing_info", "w");
+ fprintf(out, "%d\n", Num_atoms);
+ fprintf(out, "%d\n", Num_input_structures);
+ for(i = 0 ; i < Num_input_structures ; i++)
+ {
+ fprintf(out, "%lf ", aray_of_cutoff_distance[i]);
+ }
+ fprintf(out, "\n");
+ for(i = 0 ; i < (Num_input_structures - 1) ; i++)
+ {
+ fprintf(out, "%lf ", array_of_mixing_parameters[i]);
+ }
+ fprintf(out, "\n");
+ fprintf(out, "%lf\n", repulsive_sigma);
+ fprintf(out, "%lf\n", repulsive_epsilon);
+ fprintf(out, "%lf\n", fixed_value_of_force_constant);
+ fprintf(out, "%lf\n", energy_parameter_for_force_constant);
+ fprintf(out, "%lf\n", energy_difference_from_first_structure);
+ fclose(out);
+
+}
+
+void Print_en_input2(int Num_atoms, int Num_input_structures, double *aray_of_cutoff_distance, double *array_of_mixing_parameters, double repulsive_sigma, double repulsive_epsilon, double fixed_value_of_force_constant, double energy_parameter_for_force_constant, double energy_difference_from_first_structure)
+{
+ FILE *out;
+ int i;
+
+ out = fopen("out_en_boltzmann_mixing_info_2", "w");
+ fprintf(out, "%d\n", Num_atoms);
+ fprintf(out, "%d\n", Num_input_structures);
+ for(i = 0 ; i < Num_input_structures ; i++)
+ {
+ fprintf(out, "%lf ", aray_of_cutoff_distance[i]);
+ }
+ fprintf(out, "\n");
+ for(i = 0 ; i < (Num_input_structures - 1) ; i++)
+ {
+ fprintf(out, "%lf ", array_of_mixing_parameters[i]);
+ }
+ fprintf(out, "\n");
+ fprintf(out, "%lf\n", repulsive_sigma);
+ fprintf(out, "%lf\n", repulsive_epsilon);
+ fprintf(out, "%lf\n", fixed_value_of_force_constant);
+ fprintf(out, "%lf\n", energy_parameter_for_force_constant);
+ fprintf(out, "%lf\n", energy_difference_from_first_structure);
+ fclose(out);
+
+}
+
+
+/* Allocate memory for all the data structures needed for elastic network Hamiltonian*/
+void Alloc_en(int Num_atoms, int Num_input_structures, double ****array_of_pair_distance_matrices, double ****array_of_cutoff_matrices, double ***force_constants_all_pairs, double ***sigmas_for_repulsive_part, double ***epsilons_for_repulsive_part, FR_DAT **coordinates_all_structures)
+{
+ int a, i;
+
+ *array_of_pair_distance_matrices = (double ***)malloc(Num_input_structures * sizeof(double**));
+ *array_of_cutoff_matrices = (double ***)malloc(Num_input_structures * sizeof(double**));
+ *coordinates_all_structures = (FR_DAT *)malloc(Num_input_structures * sizeof(FR_DAT));
+
+
+ for(a = 0 ; a < Num_input_structures ; a++)
+ {
+ (*array_of_pair_distance_matrices)[a] = (double **)malloc(Num_atoms * sizeof(double*));
+ (*array_of_cutoff_matrices)[a] = (double **)malloc(Num_atoms * sizeof(double*));
+ (*coordinates_all_structures)[a].x = (rvec*)malloc(Num_atoms * sizeof(rvec));
+ (*coordinates_all_structures)[a].f = (rvec*)malloc(Num_atoms * sizeof(rvec));
+
+ (*coordinates_all_structures)[a].natoms = Num_atoms;
+
+ for(i = 0 ; i < Num_atoms ; i++)
+ {
+ (*array_of_pair_distance_matrices)[a][i] = (double *)malloc(Num_atoms * sizeof(double));
+ (*array_of_cutoff_matrices)[a][i] = (double *)malloc(Num_atoms * sizeof(double));
+ }
+ }
+
+ *sigmas_for_repulsive_part = (double **)malloc(Num_atoms * sizeof(double*));
+ *epsilons_for_repulsive_part = (double **)malloc(Num_atoms * sizeof(double*));
+ *force_constants_all_pairs = (double **)malloc(Num_atoms * sizeof(double*));
+ for(i = 0 ; i < Num_atoms ; i++)
+ {
+ (*sigmas_for_repulsive_part)[i] = (double *)malloc(Num_atoms * sizeof(double));
+ (*epsilons_for_repulsive_part)[i] = (double *)malloc(Num_atoms * sizeof(double));
+ (*force_constants_all_pairs)[i] = (double *)malloc(Num_atoms * sizeof(double));
+ }
+
+}
+
+
+/* Read one structure
+ * Format:
+ * Each line should have x, y, and z cooridnates of one particle (C_ALPHA) separated by white space.
+ * Number of lines should be equal to the number of particles.
+ * Returns the number of lines read. If file is in proper format this should be equal to the number of atoms.
+ * If more lines are present reads first n lines where n is the number of atoms. If less than required number of atoms
+ * found gives error and quits..*/
+int Read_one_structure(FR_DAT *one_coordinate_set, char filename[1000])
+{
+ char line[1000000];
+ int Num_lines;
+ double x, y, z;
+ FILE *in;
+ in = fopen(filename, "r");
+ if(in == NULL)
+ {
+ printf("File '%s' not found\n", filename);
+ exit(1);
+ }
+ Num_lines = 0;
+ while(fgets(line, 1000000, in) != NULL)
+ {
+ if((Num_lines + 1) > one_coordinate_set->natoms)
+ {
+ printf("Number of atoms in file '%s' is more than the expected number of %d. Something is wrong.\n", filename, one_coordinate_set->natoms);
+ exit(1);
+ }
+ sscanf(line, "%lf %lf %lf", &x, &y, &z);
+ one_coordinate_set->x[Num_lines][0] = x;
+ one_coordinate_set->x[Num_lines][1] = y;
+ one_coordinate_set->x[Num_lines][2] = z;
+ Num_lines = Num_lines + 1;
+ }
+ fclose(in);
+ /*Check if number of lines is less than number of atoms*/
+ if(Num_lines < one_coordinate_set->natoms)
+ {
+ printf("Number of lines in file '%s' (%d) is less than the expected number of atoms (%d).\n", filename, Num_lines, one_coordinate_set->natoms);
+ exit(1);
+ }
+ else
+ {
+ return Num_lines;
+ }
+}
+
+
+void Write_one_structure(FR_DAT one_coordinate_set, char filename[1000])
+{
+ FILE *out;
+ int i;
+
+ out = fopen(filename, "w");
+ for(i = 0 ; i < one_coordinate_set.natoms; i++)
+ {
+ fprintf(out, "%lf %lf %lf\n", one_coordinate_set.x[i][0], one_coordinate_set.x[i][1], one_coordinate_set.x[i][2]);
+ }
+ fclose(out);
+}
+
+
+/* Read all input structures.
+ * Input structures should be named as 'input_structures_1', 'input_structures_2',...*/
+void Read_input_structures(int Num_input_structures, FR_DAT **coordinates_all_structures)
+{
+ int i;
+ char filename[1000];
+ int num_atoms;
+ for(i = 0 ; i < Num_input_structures ; i++)
+ {
+ sprintf(filename, "INPUT_STRUCTURE_%d", (i+1));
+ num_atoms = Read_one_structure(&(*coordinates_all_structures)[i], filename);
+ }
+}
+
+void Read_input_structures2(int Num_input_structures, FR_DAT **coordinates_all_structures)
+{
+ int i;
+ char filename[1000];
+ int num_atoms;
+ for(i = 0 ; i < Num_input_structures ; i++)
+ {
+ sprintf(filename, "INPUT_STRUCTURE_2_%d", (i+1));
+ num_atoms = Read_one_structure(&(*coordinates_all_structures)[i], filename);
+ }
+}
+
+
+/* Calculaes simple distance, square of distance and the distance vector
+ * between two points in d-dimension. *point_1 and *point_2 are
+ * d-diemnsional arrays (or d-dimensional vectors). This is meant for non-periodic systems
+ * The distance_vector = point_2 - point_1*/
+void Calc_simple_distance(int dimension, double *point_1, double *point_2, double *distance, double *distance_squared, double *distance_vector)
+{
+ int i;
+ for(i=0;i<dimension;i++)
+ {
+ distance_vector[i] = point_2[i] - point_1[i];
+ }
+ *distance_squared = 0.0;
+ for(i=0;i<dimension;i++)
+ {
+ *distance_squared = *distance_squared + (distance_vector[i] * distance_vector[i]);
+ }
+ *distance = sqrt(*distance_squared);
+}
+
+
+
+/* Calculate the pair distances in all the structures or states.*/
+void Calc_pair_distances_all_structures(int Num_atoms, int Num_input_structures, FR_DAT *coordinates_all_structures, double ***array_of_pair_distance_matrices)
+{
+ int a, i, j;
+ int dimension = DIMENSION;
+ double distance;
+ double distance_squared;
+ double distance_vector[DIMENSION];
+ /*set diagonal elemnts to -1*/
+ for(a = 0 ; a < Num_input_structures ; a++)
+ {
+ for(i = 0 ; i < Num_atoms ; i++)
+ {
+ array_of_pair_distance_matrices[a][i][i] = -1.0;
+ }
+ }
+ /* calcualte pair distances*/
+ for(a = 0 ; a < Num_input_structures ; a++)
+ {
+ for(i = 0 ; i < (Num_atoms - 1) ; i++)
+ {
+ for(j = (i + 1) ; j < Num_atoms ; j++)
+ {
+ /*calculate distance*/
+ Calc_simple_distance(dimension, coordinates_all_structures[a].x[i], coordinates_all_structures[a].x[j], &distance, &distance_squared, distance_vector);
+ array_of_pair_distance_matrices[a][i][j] = distance;
+ array_of_pair_distance_matrices[a][j][i] = distance;
+ }
+ }
+ }
+
+}
+
+
+/* Print distances*/
+void Print_pair_distances_all_structures(int Num_atoms, int Num_input_structures, double ***array_of_pair_distance_matrices)
+{
+ FILE *out;
+ int a, i, j;
+ char filename[1000];
+ for(a = 0 ; a < Num_input_structures ; a++)
+ {
+ sprintf(filename, "pair_distances_%d", (a+1));
+ out = fopen(filename, "w");
+ for(i = 0 ; i < Num_atoms ; i++)
+ {
+ for(j = 0 ; j < Num_atoms ; j++)
+ {
+ fprintf(out, "%lf ", array_of_pair_distance_matrices[a][i][j]);
+ }
+ fprintf(out, "\n");
+ }
+ fclose(out);
+ }
+
+}
+
+void Print_pair_distances_all_structures2(int Num_atoms, int Num_input_structures, double ***array_of_pair_distance_matrices)
+{
+ FILE *out;
+ int a, i, j;
+ char filename[1000];
+ for(a = 0 ; a < Num_input_structures ; a++)
+ {
+ sprintf(filename, "pair_distances_2_%d", (a+1));
+ out = fopen(filename, "w");
+ for(i = 0 ; i < Num_atoms ; i++)
+ {
+ for(j = 0 ; j < Num_atoms ; j++)
+ {
+ fprintf(out, "%lf ", array_of_pair_distance_matrices[a][i][j]);
+ }
+ fprintf(out, "\n");
+ }
+ fclose(out);
+ }
+
+}
+
+
+/* Set various quantities like cutoffs, sigma, epsilons etc.*/
+void Set_various_quantities(int Num_atoms, int Num_input_structures, double ***array_of_cutoff_matrices, double **sigmas_for_repulsive_part, double **epsilons_for_repulsive_part, double *aray_of_cutoff_distances, double repulsive_sigma, double repulsive_epsilon)
+{
+ int a, i, j;
+
+ for(a = 0 ; a < Num_input_structures ; a++)
+ {
+ for(i = 0 ; i < (Num_atoms - 1) ; i++)
+ {
+ array_of_cutoff_matrices[a][i][i] = -1.0;
+ }
+ }
+
+ for(a = 0 ; a < Num_input_structures ; a++)
+ {
+ for(i = 0 ; i < (Num_atoms - 1) ; i++)
+ {
+ for(j = (i + 1) ; j < Num_atoms ; j++)
+ {
+ array_of_cutoff_matrices[a][i][j] = aray_of_cutoff_distances[a];
+ array_of_cutoff_matrices[a][j][i] = aray_of_cutoff_distances[a];
+ }
+ }
+ }
+
+
+ for(i = 0 ; i < Num_atoms ; i++)
+ {
+ sigmas_for_repulsive_part[i][i] = -1.0;
+ epsilons_for_repulsive_part[i][i] = -1.0;
+ }
+ for(i = 0 ; i < (Num_atoms - 1) ; i++)
+ {
+ for(j = (i + 1) ; j < Num_atoms ; j++)
+ {
+ sigmas_for_repulsive_part[i][j] = repulsive_sigma;
+ sigmas_for_repulsive_part[j][i] = repulsive_sigma;
+
+ epsilons_for_repulsive_part[i][j] = repulsive_epsilon;
+ epsilons_for_repulsive_part[j][i] = repulsive_epsilon;
+ }
+ }
+
+
+}
+
+
+/* Find minimum of two numbers.*/
+double Find_minimum(double number_1, double number_2)
+{
+ double min_value;
+ if(number_1 <= number_2)
+ {
+ min_value = number_1;
+ }
+ else
+ {
+ min_value = number_2;
+ }
+
+ return min_value;
+}
+
+/* Set force constants. Site dependent force constants. This is taken from Pan et al. J. Phys. Chem. B. 112, 3432
+ * (2008) (the swarms paper). They took it from some other paper.
+ *
+ * This is for tw ostate model. Generalizations probably exist.
+ * k_{ij} = \min{k^{\hat}_{ij}, 0.2 kcal mol^{-1} \AA^{-2}} where
+ * k^{\hat}_{ij} = \epsilon_k / (r_{ij}^A - r_{ij}^B)^2 . r_{ij}^A and r_{ij}^B are the distances between sites i
+ * and j in structres A and B respectively.
+ * \epsilon_k = 0.5 kcal/mol in Pan's paper.
+ * 'energy_parameter' is \epsilon_k
+ * 'fixed_value_of_force_constant' = 0.2 kcal mol^{-1} \AA^{-2}} in Pan's paper.
+ * */
+void Set_site_dependent_force_constant_2_state(int Num_input_structures, int Num_atoms, double ***array_of_pair_distance_matrices, double energy_parameter, double fixed_value_of_force_constant, double **force_constants_all_pairs)
+{
+ int i, j;
+ double force_constant_from_data, final_force_constant;
+ double distance_structure_1, distance_structure_2;
+ double temp, temp1;
+
+ for(i = 0 ; i < Num_atoms ; i++)
+ {
+ force_constants_all_pairs[i][i] = -1.0;
+ }
+ for(i = 0 ; i < (Num_atoms - 1) ; i++)
+ {
+ for(j = (i + 1) ; j < Num_atoms ; j++)
+ {
+ distance_structure_1 = array_of_pair_distance_matrices[0][i][j];
+ distance_structure_2 = array_of_pair_distance_matrices[1][i][j];
+
+ temp = distance_structure_1 - distance_structure_2;
+ temp1 = pow(temp, 2);
+ force_constant_from_data = energy_parameter / temp1;
+ final_force_constant = Find_minimum(force_constant_from_data, fixed_value_of_force_constant);
+
+ force_constants_all_pairs[i][j] = final_force_constant;
+ force_constants_all_pairs[j][i] = final_force_constant;
+ }
+ }
+}
+
+
+void Print_force_constants(int Num_atoms, double **force_constants_all_pairs)
+{
+ int i, j;
+ FILE *out;
+ out = fopen("force_constants_out", "w");
+ for(i = 0 ; i < Num_atoms ; i++)
+ {
+ for(j = 0 ; j < Num_atoms ; j++)
+ {
+ fprintf(out, "%lf ", force_constants_all_pairs[i][j]);
+ }
+ fprintf(out, "\n");
+ }
+ fclose(out);
+
+}
+
+void Print_force_constants2(int Num_atoms, double **force_constants_all_pairs)
+{
+ int i, j;
+ FILE *out;
+ out = fopen("force_constants_out_2", "w");
+ for(i = 0 ; i < Num_atoms ; i++)
+ {
+ for(j = 0 ; j < Num_atoms ; j++)
+ {
+ fprintf(out, "%lf ", force_constants_all_pairs[i][j]);
+ }
+ fprintf(out, "\n");
+ }
+ fclose(out);
+
+}
+
+
+/** Codes for force and energy calcualtion**/
+
+/* Calculates scalar force and energy for one pair of sites.
+ * The functional form:
+ * U_R(r_{ij}) = \epsilon (\sigma / r_{ij})^n
+ * n = 12*/
+void Cal_repulsive_force_pot_one_pair(double distance, int index_of_site_1, int index_of_site_2, double **sigmas_for_repulsive_part, double **epsilons_for_repulsive_part, int index_of_the_repulsive_function, double *scalar_force, double *potential)
+{
+ int i, j, n;
+ double sigma, epsilon, sigma_over_distance;
+ i = index_of_site_1;
+ j = index_of_site_2;
+ n = index_of_the_repulsive_function;
+ sigma = sigmas_for_repulsive_part[i][j];
+ epsilon = epsilons_for_repulsive_part[i][j];
+ sigma_over_distance = sigma / distance;
+
+ *potential = epsilon * pow(sigma_over_distance, n);
+ *scalar_force = (*potential) * ( ((double)n) / distance );
+
+}
+
+/* Calcualte the force and potential for one pair for one structure. This function is only called
+ * when two sites are within interacting distance in the native structure.I.e. if the distance between
+ * two sites in the structure is less than the cutoff for that struture.*/
+void get_force_one_pair_one_structure(double distance, int index_of_site_1, int index_of_site_2, int index_of_input_structure, double ***array_of_pair_distance_matrices, double **force_constants_all_pairs, double *scalar_force, double *potential)
+{
+ double k, diff, distance_in_static_structure;
+
+ k = force_constants_all_pairs[index_of_site_1][index_of_site_2];
+ distance_in_static_structure = array_of_pair_distance_matrices[index_of_input_structure][index_of_site_1][index_of_site_2];
+
+ diff = distance - distance_in_static_structure;
+
+ *potential = 0.5 * k * pow(diff, 2);
+ *scalar_force = -k * diff;
+}
+
+
+
+
+/* Calculate the total forces on all the particles as well as the total potential energy*/
+void getforces(FR_DAT *fr, FR_DAT **coordinates_all_structures, int Num_input_structures, double ***array_of_pair_distance_matrices, double **force_constants_all_pairs, double **sigmas_for_repulsive_part, double **epsilons_for_repulsive_part, double *array_of_mixing_parameters, double *aray_of_cutoff_distances, double energy_difference_from_first_structure)
+{
+ int a, i, j, d;
+ double distance, distance_squared, scalar_force_repulsive, potential_repulsive;
+ double scalar_force_one_structure, potential_one_structure;
+ double distance_vector[3];
+ double unit_vector[3];
+ double temp_force[3]; /*this is used for various stages of force calculation*/
+ double beta_m; /*Mixing parameter*/
+ double *Boltzmann_factor_like_terms; /* one for each structure*/
+ double temp; /*for miscellenious purposes*/
+ double sum_of_Boltzmann_factors;
+ double *factor_for_force_for_each_structure;
+
+ beta_m = array_of_mixing_parameters[0]; /*two input structures. Only one mixing parameter*/
+
+ Boltzmann_factor_like_terms = (double*)malloc(Num_input_structures * sizeof(double));
+ factor_for_force_for_each_structure = (double*)malloc(Num_input_structures * sizeof(double));
+
+ /* zero froces for the current configuration (or frame) */
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ for(d = 0 ; d < 3 ; d++)
+ {
+ fr->f[i][d] = 0.0;
+ }
+ }
+
+ /* zero forces for data structure that stores forces from each individual structure*/
+ for(a = 0 ; a < Num_input_structures ; a++)
+ {
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ for(d = 0 ; d < 3 ; d++)
+ {
+ (*coordinates_all_structures)[a].f[i][d] = 0.0;
+ }
+ }
+ (*coordinates_all_structures)[a].U = 0.0;
+ }
+
+ /* zero total energy*/
+ fr->U = 0.0;
+ fr->U_r = 0.0;
+ fr->U_en = 0.0;
+
+ /* double loop over all possible pairs */
+ for(i = 0 ; i < (fr->natoms - 1) ; i++)
+ {
+ for(j = (i+1) ; j < fr->natoms ; j++)
+ {
+ /* calculate distance and unit vector*/
+ Calc_simple_distance(3, fr->x[i], fr->x[j], &distance, &distance_squared, distance_vector);
+ for(d = 0 ; d < 3 ; d++)
+ {
+ unit_vector[d] = distance_vector[d] / distance;
+ }
+ /* Calculate force and potential from the repulsive part and sum
+ these forces and potential for both the sites into the main data structure*/
+ Cal_repulsive_force_pot_one_pair(distance, i, j, sigmas_for_repulsive_part, epsilons_for_repulsive_part, 12, &scalar_force_repulsive, &potential_repulsive);
+ fr->U = fr->U + potential_repulsive;
+ fr->U_r = fr->U_r + potential_repulsive;
+ for(d = 0 ; d < 3 ; d++)
+ {
+ temp_force[d] = scalar_force_repulsive * unit_vector[d];
+ fr->f[i][d] = fr->f[i][d] + (-temp_force[d]);
+ fr->f[j][d] = fr->f[j][d] + temp_force[d];
+ }
+
+ /* loop over all the structure and calculate and sum force and potential for each
+ structure in separate data structures.*/
+ for(a = 0 ; a < Num_input_structures ; a++)
+ {
+ /*first check for cutoff. I.e. calculate interaction only if the pair distance
+ between two sites in question in the static structure is less than the cutoff
+ for that structure.*/
+ if(array_of_pair_distance_matrices[a][i][j] < aray_of_cutoff_distances[a])
+ {
+ get_force_one_pair_one_structure(distance, i, j, a, array_of_pair_distance_matrices, force_constants_all_pairs, &scalar_force_one_structure, &potential_one_structure);
+ (*coordinates_all_structures)[a].U = (*coordinates_all_structures)[a].U + potential_one_structure;
+ for(d = 0 ; d < 3 ; d++)
+ {
+ temp_force[d] = scalar_force_one_structure * unit_vector[d];
+ (*coordinates_all_structures)[a].f[i][d] = (*coordinates_all_structures)[a].f[i][d] +
+ (-temp_force[d]);
+ (*coordinates_all_structures)[a].f[j][d] = (*coordinates_all_structures)[a].f[j][d] +
+ temp_force[d];
+ }
+ }
+ } /*end of loop over a*/
+ } /*end of j loop*/
+ } /*end of i loop*/
+
+ /* Now we have calcualted the potentials for both the structures, use them to calculate
+ constant terms. Constant terms are like Boltzmann factors where each term involves
+ the potential energy of that structure.*/
+ /* Calculate Boltzmann term*/
+ sum_of_Boltzmann_factors = 0.0;
+ /* First state*/
+ temp = -beta_m * ((*coordinates_all_structures)[0].U);
+ Boltzmann_factor_like_terms[0] = exp(temp);
+ /* Second state*/
+ temp = -beta_m * ( ((*coordinates_all_structures)[1].U) + energy_difference_from_first_structure );
+ Boltzmann_factor_like_terms[1] = exp(temp);
+ /* Sum of Boltzmann terms*/
+ sum_of_Boltzmann_factors = Boltzmann_factor_like_terms[0] + Boltzmann_factor_like_terms[1];
+ /* Calculate the constant factor for each structure that forces need to be multiplied by.*/
+ for(a = 0 ; a < Num_input_structures ; a++)
+ {
+ factor_for_force_for_each_structure[a] = Boltzmann_factor_like_terms[a] / sum_of_Boltzmann_factors;
+ }
+
+ /* Update the total forces and total forces on all the particles. It will involve a sum over
+ all the structures.*/
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ for(d = 0 ; d < 3 ; d++)
+ {
+ for(a = 0 ; a < Num_input_structures ; a++)
+ {
+ temp = factor_for_force_for_each_structure[a];
+ fr->f[i][d] = fr->f[i][d] + (temp * (*coordinates_all_structures)[a].f[i][d]);
+ }
+ }
+ }
+
+ fr->U_en = (-(1.0 / beta_m) * log(sum_of_Boltzmann_factors));
+ /* Calculate the total energy*/
+ fr->U = fr->U + (-(1.0 / beta_m) * log(sum_of_Boltzmann_factors));
+
+ free(Boltzmann_factor_like_terms);
+ free(factor_for_force_for_each_structure);
+}
+
+
+
+void getforces_cons(FR_DAT *fr, FR_DAT **coordinates_all_structures, int Num_input_structures, double ***array_of_pair_distance_matrices, double **force_constants_all_pairs, double **sigmas_for_repulsive_part, double **epsilons_for_repulsive_part, double *array_of_mixing_parameters, double *aray_of_cutoff_distances, double energy_difference_from_first_structure, collective_variables *cons_distances, int Num_cv, double KK)
+{
+ int a, b, i, j, d;
+ double distance, distance_squared, scalar_force_repulsive, potential_repulsive;
+ double scalar_force_one_structure, potential_one_structure;
+ double distance_vector[3];
+ double unit_vector[3];
+ double temp_force[3]; /*this is used for various stages of force calculation*/
+ double beta_m; /*Mixing parameter*/
+ double *Boltzmann_factor_like_terms; /* one for each structure*/
+ double temp; /*for miscellenious purposes*/
+ double sum_of_Boltzmann_factors;
+ double *factor_for_force_for_each_structure;
+
+ beta_m = array_of_mixing_parameters[0]; /*two input structures. Only one mixing parameter*/
+
+ Boltzmann_factor_like_terms = (double*)malloc(Num_input_structures * sizeof(double));
+ factor_for_force_for_each_structure = (double*)malloc(Num_input_structures * sizeof(double));
+
+ /* zero froces for the current configuration (or frame) */
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ for(d = 0 ; d < 3 ; d++)
+ {
+ fr->f[i][d] = 0.0;
+ }
+ }
+
+ /* zero forces for data structure that stores forces from each individual structure*/
+ for(a = 0 ; a < Num_input_structures ; a++)
+ {
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ for(d = 0 ; d < 3 ; d++)
+ {
+ (*coordinates_all_structures)[a].f[i][d] = 0.0;
+ }
+ }
+ (*coordinates_all_structures)[a].U = 0.0;
+ }
+
+ /* zero total energy*/
+ fr->U = 0.0;
+ fr->U_r = 0.0;
+ fr->U_en = 0.0;
+
+ /* double loop over all possible pairs */
+ for(i = 0 ; i < (fr->natoms - 1) ; i++)
+ {
+ for(j = (i+1) ; j < fr->natoms ; j++)
+ {
+ /* calculate distance and unit vector*/
+ Calc_simple_distance(3, fr->x[i], fr->x[j], &distance, &distance_squared, distance_vector);
+ for(d = 0 ; d < 3 ; d++)
+ {
+ unit_vector[d] = distance_vector[d] / distance;
+ }
+ /* Calculate force and potential from the repulsive part and sum
+ these forces and potential for both the sites into the main data structure*/
+ Cal_repulsive_force_pot_one_pair(distance, i, j, sigmas_for_repulsive_part, epsilons_for_repulsive_part, 12, &scalar_force_repulsive, &potential_repulsive);
+ fr->U = fr->U + potential_repulsive;
+ fr->U_r = fr->U_r + potential_repulsive;
+ for(d = 0 ; d < 3 ; d++)
+ {
+ temp_force[d] = scalar_force_repulsive * unit_vector[d];
+ fr->f[i][d] = fr->f[i][d] + (-temp_force[d]);
+ fr->f[j][d] = fr->f[j][d] + temp_force[d];
+ }
+
+ /* loop over all the structure and calculate and sum force and potential for each
+ structure in separate data structures.*/
+ for(a = 0 ; a < Num_input_structures ; a++)
+ {
+ /*first check for cutoff. I.e. calculate interaction only if the pair distance
+ between two sites in question in the static structure is less than the cutoff
+ for that structure.*/
+ if(array_of_pair_distance_matrices[a][i][j] < aray_of_cutoff_distances[a])
+ {
+ get_force_one_pair_one_structure(distance, i, j, a, array_of_pair_distance_matrices, force_constants_all_pairs, &scalar_force_one_structure, &potential_one_structure);
+ (*coordinates_all_structures)[a].U = (*coordinates_all_structures)[a].U + potential_one_structure;
+ for(d = 0 ; d < 3 ; d++)
+ {
+ temp_force[d] = scalar_force_one_structure * unit_vector[d];
+ (*coordinates_all_structures)[a].f[i][d] = (*coordinates_all_structures)[a].f[i][d] +
+ (-temp_force[d]);
+ (*coordinates_all_structures)[a].f[j][d] = (*coordinates_all_structures)[a].f[j][d] +
+ temp_force[d];
+ }
+ }
+ } /*end of loop over a*/
+ } /*end of j loop*/
+ } /*end of i loop*/
+
+ /* Now we have calcualted the potentials for both the structures, use them to calculate
+ constant terms. Constant terms are like Boltzmann factors where each term involves
+ the potential energy of that structure.*/
+ /* Calculate Boltzmann term*/
+ sum_of_Boltzmann_factors = 0.0;
+ /* First state*/
+ temp = -beta_m * ((*coordinates_all_structures)[0].U);
+ Boltzmann_factor_like_terms[0] = exp(temp);
+ /* Second state*/
+ temp = -beta_m * ( ((*coordinates_all_structures)[1].U) + energy_difference_from_first_structure );
+ Boltzmann_factor_like_terms[1] = exp(temp);
+ /* Sum of Boltzmann terms*/
+ sum_of_Boltzmann_factors = Boltzmann_factor_like_terms[0] + Boltzmann_factor_like_terms[1];
+ /* Calculate the constant factor for each structure that forces need to be multiplied by.*/
+ for(a = 0 ; a < Num_input_structures ; a++)
+ {
+ factor_for_force_for_each_structure[a] = Boltzmann_factor_like_terms[a] / sum_of_Boltzmann_factors;
+ }
+
+ /* Update the total forces and total forces on all the particles. It will involve a sum over
+ all the structures.*/
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ for(d = 0 ; d < 3 ; d++)
+ {
+ for(a = 0 ; a < Num_input_structures ; a++)
+ {
+ temp = factor_for_force_for_each_structure[a];
+ fr->f[i][d] = fr->f[i][d] + (temp * (*coordinates_all_structures)[a].f[i][d]);
+ }
+ }
+ }
+
+ /*Add constraining force*/
+ for(i=0;i<Num_cv;i++){
+
+ a = cons_distances[i].atomi;
+ b = cons_distances[i].atomj;
+ Calc_simple_distance(3, fr->x[a], fr->x[b], &distance, &distance_squared, distance_vector);
+ // printf("dis[%d][%d]=%lf\n",a+1,b+1,distance);
+ for(d = 0 ; d < 3 ; d++)
+ {
+ unit_vector[d] = distance_vector[d] / distance;
+ fr->f[a][d] += KK*unit_vector[d]*( distance - cons_distances[i].dis);
+ fr->f[b][d] += -KK*unit_vector[d]*( distance - cons_distances[i].dis);
+ }
+ }
+
+
+ fr->U_en = (-(1.0 / beta_m) * log(sum_of_Boltzmann_factors));
+ /* Calculate the total energy*/
+ fr->U = fr->U + (-(1.0 / beta_m) * log(sum_of_Boltzmann_factors));
+
+ free(Boltzmann_factor_like_terms);
+ free(factor_for_force_for_each_structure);
+}
+
+
+
+void getforces_cons_harm(FR_DAT *fr, FR_DAT **coordinates_all_structures, int Num_input_structures, double ***array_of_pair_distance_matrices, double **force_constants_all_pairs, double **sigmas_for_repulsive_part, double **epsilons_for_repulsive_part, double *array_of_mixing_parameters, double *aray_of_cutoff_distances, double energy_difference_from_first_structure, collective_variables *cons_distances, int Num_cv, FR_DAT fix_position, double KK, double Kharm)
+{
+ int a, b, i, j, d;
+ double distance, distance_squared, scalar_force_repulsive, potential_repulsive;
+ double scalar_force_one_structure, potential_one_structure;
+ double distance_vector[3];
+ double unit_vector[3];
+ double temp_force[3]; /*this is used for various stages of force calculation*/
+ double beta_m; /*Mixing parameter*/
+ double *Boltzmann_factor_like_terms; /* one for each structure*/
+ double temp; /*for miscellenious purposes*/
+ double sum_of_Boltzmann_factors;
+ double *factor_for_force_for_each_structure;
+
+ beta_m = array_of_mixing_parameters[0]; /*two input structures. Only one mixing parameter*/
+
+ Boltzmann_factor_like_terms = (double*)malloc(Num_input_structures * sizeof(double));
+ factor_for_force_for_each_structure = (double*)malloc(Num_input_structures * sizeof(double));
+
+ /* zero froces for the current configuration (or frame) */
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ for(d = 0 ; d < 3 ; d++)
+ {
+ fr->f[i][d] = 0.0;
+ }
+ }
+
+ /* zero forces for data structure that stores forces from each individual structure*/
+ for(a = 0 ; a < Num_input_structures ; a++)
+ {
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ for(d = 0 ; d < 3 ; d++)
+ {
+ (*coordinates_all_structures)[a].f[i][d] = 0.0;
+ }
+ }
+ (*coordinates_all_structures)[a].U = 0.0;
+ }
+
+ /* zero total energy*/
+ fr->U = 0.0;
+ fr->U_r = 0.0;
+ fr->U_en = 0.0;
+
+ /* double loop over all possible pairs */
+ for(i = 0 ; i < (fr->natoms - 1) ; i++)
+ {
+ for(j = (i+1) ; j < fr->natoms ; j++)
+ {
+ /* calculate distance and unit vector*/
+ Calc_simple_distance(3, fr->x[i], fr->x[j], &distance, &distance_squared, distance_vector);
+ for(d = 0 ; d < 3 ; d++)
+ {
+ unit_vector[d] = distance_vector[d] / distance;
+ }
+ /* Calculate force and potential from the repulsive part and sum
+ these forces and potential for both the sites into the main data structure*/
+ Cal_repulsive_force_pot_one_pair(distance, i, j, sigmas_for_repulsive_part, epsilons_for_repulsive_part, 12, &scalar_force_repulsive, &potential_repulsive);
+ fr->U = fr->U + potential_repulsive;
+ fr->U_r = fr->U_r + potential_repulsive;
+ for(d = 0 ; d < 3 ; d++)
+ {
+ temp_force[d] = scalar_force_repulsive * unit_vector[d];
+ fr->f[i][d] = fr->f[i][d] + (-temp_force[d]);
+ fr->f[j][d] = fr->f[j][d] + temp_force[d];
+ }
+
+ /* loop over all the structure and calculate and sum force and potential for each
+ structure in separate data structures.*/
+ for(a = 0 ; a < Num_input_structures ; a++)
+ {
+ /*first check for cutoff. I.e. calculate interaction only if the pair distance
+ between two sites in question in the static structure is less than the cutoff
+ for that structure.*/
+ if(array_of_pair_distance_matrices[a][i][j] < aray_of_cutoff_distances[a])
+ {
+ get_force_one_pair_one_structure(distance, i, j, a, array_of_pair_distance_matrices, force_constants_all_pairs, &scalar_force_one_structure, &potential_one_structure);
+ (*coordinates_all_structures)[a].U = (*coordinates_all_structures)[a].U + potential_one_structure;
+ for(d = 0 ; d < 3 ; d++)
+ {
+ temp_force[d] = scalar_force_one_structure * unit_vector[d];
+ (*coordinates_all_structures)[a].f[i][d] = (*coordinates_all_structures)[a].f[i][d] +
+ (-temp_force[d]);
+ (*coordinates_all_structures)[a].f[j][d] = (*coordinates_all_structures)[a].f[j][d] +
+ temp_force[d];
+ }
+ }
+ } /*end of loop over a*/
+ } /*end of j loop*/
+ } /*end of i loop*/
+
+ /* Now we have calcualted the potentials for both the structures, use them to calculate
+ constant terms. Constant terms are like Boltzmann factors where each term involves
+ the potential energy of that structure.*/
+ /* Calculate Boltzmann term*/
+ sum_of_Boltzmann_factors = 0.0;
+ /* First state*/
+ temp = -beta_m * ((*coordinates_all_structures)[0].U);
+ Boltzmann_factor_like_terms[0] = exp(temp);
+ /* Second state*/
+ temp = -beta_m * ( ((*coordinates_all_structures)[1].U) + energy_difference_from_first_structure );
+ Boltzmann_factor_like_terms[1] = exp(temp);
+ /* Sum of Boltzmann terms*/
+ sum_of_Boltzmann_factors = Boltzmann_factor_like_terms[0] + Boltzmann_factor_like_terms[1];
+ /* Calculate the constant factor for each structure that forces need to be multiplied by.*/
+ for(a = 0 ; a < Num_input_structures ; a++)
+ {
+ factor_for_force_for_each_structure[a] = Boltzmann_factor_like_terms[a] / sum_of_Boltzmann_factors;
+ }
+
+ /* Update the total forces and total forces on all the particles. It will involve a sum over
+ all the structures.*/
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ for(d = 0 ; d < 3 ; d++)
+ {
+ for(a = 0 ; a < Num_input_structures ; a++)
+ {
+ temp = factor_for_force_for_each_structure[a];
+ fr->f[i][d] = fr->f[i][d] + (temp * (*coordinates_all_structures)[a].f[i][d]);
+ }
+ //Add harmonic constraining force
+ fr->f[i][d] += -2*Kharm*(fr->x[i][d] - fix_position.x[i][d]);
+
+ }
+ }
+
+ /*Add constraining force*/
+ for(i=0;i<Num_cv;i++){
+
+ a = cons_distances[i].atomi;
+ b = cons_distances[i].atomj;
+ Calc_simple_distance(3, fr->x[a], fr->x[b], &distance, &distance_squared, distance_vector);
+ // printf("dis[%d][%d]=%lf\n",a+1,b+1,distance);
+ for(d = 0 ; d < 3 ; d++)
+ {
+ unit_vector[d] = distance_vector[d] / distance;
+ fr->f[a][d] += KK*unit_vector[d]*( distance - cons_distances[i].dis);
+ fr->f[b][d] += -KK*unit_vector[d]*( distance - cons_distances[i].dis);
+ }
+ }
+
+ // printf("%lf %lf\n", KK, Kharm);
+
+ fr->U_en = (-(1.0 / beta_m) * log(sum_of_Boltzmann_factors));
+ /* Calculate the total energy*/
+ fr->U = fr->U + (-(1.0 / beta_m) * log(sum_of_Boltzmann_factors));
+
+ free(Boltzmann_factor_like_terms);
+ free(factor_for_force_for_each_structure);
+}
+
+
+void getforces_harm(FR_DAT *fr, FR_DAT **coordinates_all_structures, int Num_input_structures, double ***array_of_pair_distance_matrices, double **force_constants_all_pairs, double **sigmas_for_repulsive_part, double **epsilons_for_repulsive_part, double *array_of_mixing_parameters, double *aray_of_cutoff_distances, double energy_difference_from_first_structure, FR_DAT fix_position, double Kharm)
+{
+ int a, i, j, d;
+ double distance, distance_squared, scalar_force_repulsive, potential_repulsive;
+ double scalar_force_one_structure, potential_one_structure;
+ double distance_vector[3];
+ double unit_vector[3];
+ double temp_force[3]; /*this is used for various stages of force calculation*/
+ double beta_m; /*Mixing parameter*/
+ double *Boltzmann_factor_like_terms; /* one for each structure*/
+ double temp; /*for miscellenious purposes*/
+ double sum_of_Boltzmann_factors;
+ double *factor_for_force_for_each_structure;
+
+ beta_m = array_of_mixing_parameters[0]; /*two input structures. Only one mixing parameter*/
+
+ Boltzmann_factor_like_terms = (double*)malloc(Num_input_structures * sizeof(double));
+ factor_for_force_for_each_structure = (double*)malloc(Num_input_structures * sizeof(double));
+
+ /* zero froces for the current configuration (or frame) */
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ for(d = 0 ; d < 3 ; d++)
+ {
+ fr->f[i][d] = 0.0;
+ }
+ }
+
+ /* zero forces for data structure that stores forces from each individual structure*/
+ for(a = 0 ; a < Num_input_structures ; a++)
+ {
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ for(d = 0 ; d < 3 ; d++)
+ {
+ (*coordinates_all_structures)[a].f[i][d] = 0.0;
+ }
+ }
+ (*coordinates_all_structures)[a].U = 0.0;
+ }
+
+ /* zero total energy*/
+ fr->U = 0.0;
+ fr->U_r = 0.0;
+ fr->U_en = 0.0;
+
+ /* double loop over all possible pairs */
+ for(i = 0 ; i < (fr->natoms - 1) ; i++)
+ {
+ for(j = (i+1) ; j < fr->natoms ; j++)
+ {
+ /* calculate distance and unit vector*/
+ Calc_simple_distance(3, fr->x[i], fr->x[j], &distance, &distance_squared, distance_vector);
+ for(d = 0 ; d < 3 ; d++)
+ {
+ unit_vector[d] = distance_vector[d] / distance;
+ }
+ /* Calculate force and potential from the repulsive part and sum
+ these forces and potential for both the sites into the main data structure*/
+ Cal_repulsive_force_pot_one_pair(distance, i, j, sigmas_for_repulsive_part, epsilons_for_repulsive_part, 12, &scalar_force_repulsive, &potential_repulsive);
+ fr->U = fr->U + potential_repulsive;
+ fr->U_r = fr->U_r + potential_repulsive;
+ for(d = 0 ; d < 3 ; d++)
+ {
+ temp_force[d] = scalar_force_repulsive * unit_vector[d];
+ fr->f[i][d] = fr->f[i][d] + (-temp_force[d]);
+ fr->f[j][d] = fr->f[j][d] + temp_force[d];
+ }
+
+ /* loop over all the structure and calculate and sum force and potential for each
+ structure in separate data structures.*/
+ for(a = 0 ; a < Num_input_structures ; a++)
+ {
+ /*first check for cutoff. I.e. calculate interaction only if the pair distance
+ between two sites in question in the static structure is less than the cutoff
+ for that structure.*/
+ if(array_of_pair_distance_matrices[a][i][j] < aray_of_cutoff_distances[a])
+ {
+ get_force_one_pair_one_structure(distance, i, j, a, array_of_pair_distance_matrices, force_constants_all_pairs, &scalar_force_one_structure, &potential_one_structure);
+ (*coordinates_all_structures)[a].U = (*coordinates_all_structures)[a].U + potential_one_structure;
+ for(d = 0 ; d < 3 ; d++)
+ {
+ temp_force[d] = scalar_force_one_structure * unit_vector[d];
+ (*coordinates_all_structures)[a].f[i][d] = (*coordinates_all_structures)[a].f[i][d] +
+ (-temp_force[d]);
+ (*coordinates_all_structures)[a].f[j][d] = (*coordinates_all_structures)[a].f[j][d] +
+ temp_force[d];
+ }
+ }
+ } /*end of loop over a*/
+ } /*end of j loop*/
+ } /*end of i loop*/
+
+ /* Now we have calcualted the potentials for both the structures, use them to calculate
+ constant terms. Constant terms are like Boltzmann factors where each term involves
+ the potential energy of that structure.*/
+ /* Calculate Boltzmann term*/
+ sum_of_Boltzmann_factors = 0.0;
+ /* First state*/
+ temp = -beta_m * ((*coordinates_all_structures)[0].U);
+ Boltzmann_factor_like_terms[0] = exp(temp);
+ /* Second state*/
+ temp = -beta_m * ( ((*coordinates_all_structures)[1].U) + energy_difference_from_first_structure );
+ Boltzmann_factor_like_terms[1] = exp(temp);
+ /* Sum of Boltzmann terms*/
+ sum_of_Boltzmann_factors = Boltzmann_factor_like_terms[0] + Boltzmann_factor_like_terms[1];
+ /* Calculate the constant factor for each structure that forces need to be multiplied by.*/
+ for(a = 0 ; a < Num_input_structures ; a++)
+ {
+ factor_for_force_for_each_structure[a] = Boltzmann_factor_like_terms[a] / sum_of_Boltzmann_factors;
+ }
+
+ /* Update the total forces and total forces on all the particles. It will involve a sum over
+ all the structures.*/
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ for(d = 0 ; d < 3 ; d++)
+ {
+ for(a = 0 ; a < Num_input_structures ; a++)
+ {
+ temp = factor_for_force_for_each_structure[a];
+ fr->f[i][d] = fr->f[i][d] + (temp * (*coordinates_all_structures)[a].f[i][d]);
+ }
+ //Add harmonic constraining force
+ fr->f[i][d] += -2*Kharm*(fr->x[i][d] - fix_position.x[i][d]);
+ }
+ }
+
+ fr->U_en = (-(1.0 / beta_m) * log(sum_of_Boltzmann_factors));
+ /* Calculate the total energy*/
+ fr->U = fr->U + (-(1.0 / beta_m) * log(sum_of_Boltzmann_factors));
+
+ free(Boltzmann_factor_like_terms);
+ free(factor_for_force_for_each_structure);
+}
+
+
+void getforces_cons_harm_omp(FR_DAT *fr, FR_DAT **coordinates_all_structures, int Num_input_structures, double ***array_of_pair_distance_matrices, double **force_constants_all_pairs, double **sigmas_for_repulsive_part, double **epsilons_for_repulsive_part, double *array_of_mixing_parameters, double *aray_of_cutoff_distances, double energy_difference_from_first_structure, collective_variables *cons_distances, int Num_cv, FR_DAT fix_position, double KK, double Kharm, int Num_atoms)
+{
+ int a, b, i, j, d;
+ double distance, distance_squared, scalar_force_repulsive, potential_repulsive;
+ double scalar_force_one_structure, potential_one_structure;
+ double distance_vector[3];
+ double unit_vector[3];
+ double temp_force[3]; /*this is used for various stages of force calculation*/
+ double beta_m; /*Mixing parameter*/
+ double *Boltzmann_factor_like_terms; /* one for each structure*/
+ double temp; /*for miscellenious purposes*/
+ double sum_of_Boltzmann_factors;
+ double *factor_for_force_for_each_structure;
+
+ beta_m = array_of_mixing_parameters[0]; /*two input structures. Only one mixing parameter*/
+
+ Boltzmann_factor_like_terms = (double*)malloc(Num_input_structures * sizeof(double));
+ factor_for_force_for_each_structure = (double*)malloc(Num_input_structures * sizeof(double));
+
+ /* zero froces for the current configuration (or frame) */
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ for(d = 0 ; d < 3 ; d++)
+ {
+ fr->f[i][d] = 0.0;
+ }
+ }
+
+ FR_DAT_MINI *coordinates_all_structures_mini;
+
+ coordinates_all_structures_mini = (FR_DAT_MINI *)malloc(Num_input_structures * sizeof(FR_DAT_MINI));
+
+ for(a=0; a< Num_input_structures; a++){
+ coordinates_all_structures_mini[a].f = (rvec*)malloc(Num_atoms * sizeof(rvec));
+ }
+
+
+ /* zero forces for data structure that stores forces from each individual structure*/
+ for(a = 0 ; a < Num_input_structures ; a++)
+ {
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ for(d = 0 ; d < 3 ; d++)
+ {
+ coordinates_all_structures_mini[a].f[i][d] = 0.0;
+ }
+ }
+ coordinates_all_structures_mini[a].U = 0.0;
+ }
+
+ /* zero total energy*/
+ fr->U = 0.0;
+ fr->U_r = 0.0;
+ fr->U_en = 0.0;
+
+ /* double loop over all possible pairs */
+ for(i = 0 ; i < (fr->natoms - 1) ; i++)
+ {
+ for(j = (i+1) ; j < fr->natoms ; j++)
+ {
+ /* calculate distance and unit vector*/
+ Calc_simple_distance(3, fr->x[i], fr->x[j], &distance, &distance_squared, distance_vector);
+ for(d = 0 ; d < 3 ; d++)
+ {
+ unit_vector[d] = distance_vector[d] / distance;
+ }
+ /* Calculate force and potential from the repulsive part and sum
+ these forces and potential for both the sites into the main data structure*/
+ //ADD THRESHOLD
+ //
+ //CHANGE POWER
+ //if(distance > 1.8){
+ Cal_repulsive_force_pot_one_pair(distance, i, j, sigmas_for_repulsive_part, epsilons_for_repulsive_part, 2, &scalar_force_repulsive, &potential_repulsive);
+ //}
+ //else {
+ //Cal_repulsive_force_pot_one_pair(distance, i, j, sigmas_for_repulsive_part, epsilons_for_repulsive_part, 2, &scalar_force_repulsive, &potential_repulsive);
+ //scalar_force_repulsive=0;
+ //potential_repulsive=0;
+ //}
+ //printf("test scalar force %f atom: %d %d\n", scalar_force_repulsive, i, j);
+ //fflush(stdout);
+
+ fr->U = fr->U + potential_repulsive;
+ fr->U_r = fr->U_r + potential_repulsive;
+ for(d = 0 ; d < 3 ; d++)
+ {
+ temp_force[d] = scalar_force_repulsive * unit_vector[d];
+ fr->f[i][d] = fr->f[i][d] + (-temp_force[d]);
+ fr->f[j][d] = fr->f[j][d] + temp_force[d];
+ }
+
+ /* loop over all the structure and calculate and sum force and potential for each
+ structure in separate data structures.*/
+ for(a = 0 ; a < Num_input_structures ; a++)
+ {
+ /*first check for cutoff. I.e. calculate interaction only if the pair distance
+ between two sites in question in the static structure is less than the cutoff
+ for that structure.*/
+ if(array_of_pair_distance_matrices[a][i][j] < aray_of_cutoff_distances[a])
+ {
+
+ // if(array_of_pair_distance_matrices[a][i][j]>3.6){
+ get_force_one_pair_one_structure(distance, i, j, a, array_of_pair_distance_matrices, force_constants_all_pairs, &scalar_force_one_structure, &potential_one_structure);
+ // }
+ // else{
+ // scalar_force_one_structure=0;
+ // potential_one_structure=0;
+
+ // }
+
+ //printf("test scalar force %f atom: %d %d\n", scalar_force_one_structure, i, j);
+ //fflush(stdout);
+
+
+ coordinates_all_structures_mini[a].U = coordinates_all_structures_mini[a].U + potential_one_structure;
+ for(d = 0 ; d < 3 ; d++)
+ {
+ temp_force[d] = scalar_force_one_structure * unit_vector[d];
+ coordinates_all_structures_mini[a].f[i][d] = coordinates_all_structures_mini[a].f[i][d] +
+ (-temp_force[d]);
+ coordinates_all_structures_mini[a].f[j][d] = coordinates_all_structures_mini[a].f[j][d] +
+ temp_force[d];
+ }
+ }
+ } /*end of loop over a*/
+ } /*end of j loop*/
+ } /*end of i loop*/
+
+ /* Now we have calcualted the potentials for both the structures, use them to calculate
+ constant terms. Constant terms are like Boltzmann factors where each term involves
+ the potential energy of that structure.*/
+ /* Calculate Boltzmann term*/
+ sum_of_Boltzmann_factors = 0.0;
+ /* First state*/
+ temp = -beta_m * (coordinates_all_structures_mini[0].U);
+ //printf("test temp %f atom: %d\n", temp, i);
+ //fflush(stdout);
+ Boltzmann_factor_like_terms[0] = exp(temp);
+ /* Second state*/
+ temp = -beta_m * ( (coordinates_all_structures_mini[1].U) + energy_difference_from_first_structure );
+ Boltzmann_factor_like_terms[1] = exp(temp);
+ /* Sum of Boltzmann terms*/
+ sum_of_Boltzmann_factors = Boltzmann_factor_like_terms[0] + Boltzmann_factor_like_terms[1];
+ /* Calculate the constant factor for each structure that forces need to be multiplied by.*/
+ for(a = 0 ; a < Num_input_structures ; a++)
+ {
+ factor_for_force_for_each_structure[a] = Boltzmann_factor_like_terms[a] / sum_of_Boltzmann_factors;
+ }
+
+ /* Update the total forces and total forces on all the particles. It will involve a sum over
+ all the structures.*/
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ for(d = 0 ; d < 3 ; d++)
+ {
+ for(a = 0 ; a < Num_input_structures ; a++)
+ {
+ temp = factor_for_force_for_each_structure[a];
+ fr->f[i][d] = fr->f[i][d] + (temp * coordinates_all_structures_mini[a].f[i][d]);
+
+ }
+ //Add harmonic constraining force
+ fr->f[i][d] += -2*Kharm*(fr->x[i][d] - fix_position.x[i][d]);
+ // printf("force test %f\n", fr->f[i][d]);
+ // fflush(stdout);
+
+ }
+ }
+
+ // printf("force test %f\n", fr->f[13][1]);
+ // fflush(stdout);
+ /*Add constraining force*/
+ for(i=0;i<Num_cv;i++){
+
+ a = cons_distances[i].atomi;
+ b = cons_distances[i].atomj;
+ Calc_simple_distance(3, fr->x[a], fr->x[b], &distance, &distance_squared, distance_vector);
+ for(d = 0 ; d < 3 ; d++)
+ {
+ unit_vector[d] = distance_vector[d] / distance;
+ fr->f[a][d] += KK*unit_vector[d]*( distance - cons_distances[i].dis);
+ fr->f[b][d] += -KK*unit_vector[d]*( distance - cons_distances[i].dis);
+ }
+ //if(i%500==0) printf("force test2 %lf\n", fr->f[a][1]);
+ //fflush(stdout);
+ }
+
+ // printf("%lf %lf\n", KK, Kharm);
+
+ fr->U_en = (-(1.0 / beta_m) * log(sum_of_Boltzmann_factors));
+ /* Calculate the total energy*/
+ fr->U = fr->U + (-(1.0 / beta_m) * log(sum_of_Boltzmann_factors));
+
+ free(Boltzmann_factor_like_terms);
+ free(factor_for_force_for_each_structure);
+
+ for(a=0; a<Num_input_structures;a++)
+ free(coordinates_all_structures_mini[a].f);
+ free(coordinates_all_structures_mini);
+}
+
+
+void getforces_harm_omp(FR_DAT *fr, FR_DAT **coordinates_all_structures, int Num_input_structures, double ***array_of_pair_distance_matrices, double **force_constants_all_pairs, double **sigmas_for_repulsive_part, double **epsilons_for_repulsive_part, double *array_of_mixing_parameters, double *aray_of_cutoff_distances, double energy_difference_from_first_structure, FR_DAT fix_position, double Kharm, int Num_atoms)
+{
+ int a, i, j, d;
+ double distance, distance_squared, scalar_force_repulsive, potential_repulsive;
+ double scalar_force_one_structure, potential_one_structure;
+ double distance_vector[3];
+ double unit_vector[3];
+ double temp_force[3]; /*this is used for various stages of force calculation*/
+ double beta_m; /*Mixing parameter*/
+ double *Boltzmann_factor_like_terms; /* one for each structure*/
+ double temp; /*for miscellenious purposes*/
+ double sum_of_Boltzmann_factors;
+ double *factor_for_force_for_each_structure;
+
+ beta_m = array_of_mixing_parameters[0]; /*two input structures. Only one mixing parameter*/
+
+ Boltzmann_factor_like_terms = (double*)malloc(Num_input_structures * sizeof(double));
+ factor_for_force_for_each_structure = (double*)malloc(Num_input_structures * sizeof(double));
+
+ FR_DAT_MINI *coordinates_all_structures_mini;
+
+ coordinates_all_structures_mini = (FR_DAT_MINI *)malloc(Num_input_structures * sizeof(FR_DAT_MINI));
+
+ for(a=0; a< Num_input_structures; a++){
+ coordinates_all_structures_mini[a].f = (rvec*)malloc(Num_atoms * sizeof(rvec));
+ }
+
+ /* zero froces for the current configuration (or frame) */
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ for(d = 0 ; d < 3 ; d++)
+ {
+ fr->f[i][d] = 0.0;
+ }
+ }
+
+ /* zero forces for data structure that stores forces from each individual structure*/
+ for(a = 0 ; a < Num_input_structures ; a++)
+ {
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ for(d = 0 ; d < 3 ; d++)
+ {
+ coordinates_all_structures_mini[a].f[i][d] = 0.0;
+ }
+ }
+ coordinates_all_structures_mini[a].U = 0.0;
+ }
+
+ /* zero total energy*/
+ fr->U = 0.0;
+ fr->U_r = 0.0;
+ fr->U_en = 0.0;
+
+ /* double loop over all possible pairs */
+ for(i = 0 ; i < (fr->natoms - 1) ; i++)
+ {
+ for(j = (i+1) ; j < fr->natoms ; j++)
+ {
+ /* calculate distance and unit vector*/
+ Calc_simple_distance(3, fr->x[i], fr->x[j], &distance, &distance_squared, distance_vector);
+ for(d = 0 ; d < 3 ; d++)
+ {
+ unit_vector[d] = distance_vector[d] / distance;
+ }
+ /* Calculate force and potential from the repulsive part and sum
+ these forces and potential for both the sites into the main data structure*/
+ //ADD THRESHOLD
+ //
+ //CHANGE POWER
+ //if(distance > 1.8){
+ Cal_repulsive_force_pot_one_pair(distance, i, j, sigmas_for_repulsive_part, epsilons_for_repulsive_part, 2, &scalar_force_repulsive, &potential_repulsive);
+ //}
+ //else {
+ //Cal_repulsive_force_pot_one_pair(distance, i, j, sigmas_for_repulsive_part, epsilons_for_repulsive_part, 2, &scalar_force_repulsive, &potential_repulsive);
+ //scalar_force_repulsive=0;
+ //potential_repulsive=0;
+ //}
+ // printf("test scalar force2 %f atom: %d %d\n", scalar_force_repulsive, i, j);
+ // fflush(stdout);
+ fr->U = fr->U + potential_repulsive;
+ fr->U_r = fr->U_r + potential_repulsive;
+ for(d = 0 ; d < 3 ; d++)
+ {
+ temp_force[d] = scalar_force_repulsive * unit_vector[d];
+ fr->f[i][d] = fr->f[i][d] + (-temp_force[d]);
+ fr->f[j][d] = fr->f[j][d] + temp_force[d];
+ }
+
+ /* loop over all the structure and calculate and sum force and potential for each
+ structure in separate data structures.*/
+ for(a = 0 ; a < Num_input_structures ; a++)
+ {
+ /*first check for cutoff. I.e. calculate interaction only if the pair distance
+ between two sites in question in the static structure is less than the cutoff
+ for that structure.*/
+ if(array_of_pair_distance_matrices[a][i][j] < aray_of_cutoff_distances[a])
+ {
+ get_force_one_pair_one_structure(distance, i, j, a, array_of_pair_distance_matrices, force_constants_all_pairs, &scalar_force_one_structure, &potential_one_structure);
+ // printf("test potential %f atom: %d %d\n", potential_one_structure, i, j);
+ // fflush(stdout);
+ coordinates_all_structures_mini[a].U = coordinates_all_structures_mini[a].U + potential_one_structure;
+ for(d = 0 ; d < 3 ; d++)
+ {
+ temp_force[d] = scalar_force_one_structure * unit_vector[d];
+ coordinates_all_structures_mini[a].f[i][d] = coordinates_all_structures_mini[a].f[i][d] +
+ (-temp_force[d]);
+ coordinates_all_structures_mini[a].f[j][d] = coordinates_all_structures_mini[a].f[j][d] +
+ temp_force[d];
+ }
+ }
+ } /*end of loop over a*/
+ } /*end of j loop*/
+ } /*end of i loop*/
+
+ /* Now we have calcualted the potentials for both the structures, use them to calculate
+ constant terms. Constant terms are like Boltzmann factors where each term involves
+ the potential energy of that structure.*/
+ /* Calculate Boltzmann term*/
+ sum_of_Boltzmann_factors = 0.0;
+ /* First state*/
+ temp = -beta_m * (coordinates_all_structures_mini[0].U);
+ //printf("test temp2 %f atom: %d\n", temp, i);
+ //fflush(stdout);
+ Boltzmann_factor_like_terms[0] = exp(temp);
+ /* Second state*/
+ temp = -beta_m * ( (coordinates_all_structures_mini[1].U) + energy_difference_from_first_structure );
+ Boltzmann_factor_like_terms[1] = exp(temp);
+ /* Sum of Boltzmann terms*/
+ sum_of_Boltzmann_factors = Boltzmann_factor_like_terms[0] + Boltzmann_factor_like_terms[1];
+ /* Calculate the constant factor for each structure that forces need to be multiplied by.*/
+ for(a = 0 ; a < Num_input_structures ; a++)
+ {
+ factor_for_force_for_each_structure[a] = Boltzmann_factor_like_terms[a] / sum_of_Boltzmann_factors;
+ }
+
+ /* Update the total forces and total forces on all the particles. It will involve a sum over
+ all the structures.*/
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ for(d = 0 ; d < 3 ; d++)
+ {
+ for(a = 0 ; a < Num_input_structures ; a++)
+ {
+ temp = factor_for_force_for_each_structure[a];
+ fr->f[i][d] = fr->f[i][d] + (temp * coordinates_all_structures_mini[a].f[i][d]);
+ }
+ //Add harmonic constraining force
+ fr->f[i][d] += -2*Kharm*(fr->x[i][d] - fix_position.x[i][d]);
+ }
+ }
+
+ fr->U_en = (-(1.0 / beta_m) * log(sum_of_Boltzmann_factors));
+ /* Calculate the total energy*/
+ fr->U = fr->U + (-(1.0 / beta_m) * log(sum_of_Boltzmann_factors));
+
+ free(Boltzmann_factor_like_terms);
+ free(factor_for_force_for_each_structure);
+ for(a=0; a<Num_input_structures;a++)
+ free(coordinates_all_structures_mini[a].f);
+ free(coordinates_all_structures_mini);
+}
+
+
+
+
Added: SwiftApps/CMTS/stringmethod/src/en_boltzmann_mixing_stuff.h
===================================================================
--- SwiftApps/CMTS/stringmethod/src/en_boltzmann_mixing_stuff.h (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/en_boltzmann_mixing_stuff.h 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,54 @@
+/*All routines needed for two state or multistate elastic network based Hamiltonian.*/
+
+#ifndef _en_boltzmann_mixing_stuff_h
+#define _en_boltzmann_mixing_stuff_h
+
+#include "md_ld_common_d_dimension_namd.h"
+
+void Read_en_info(int *Num_atoms, int *Num_input_structures, double **aray_of_cutoff_distance, double **array_of_mixing_parameters, double *repulsive_sigma, double *repulsive_epsilon, double *fixed_value_of_force_constant, double *energy_parameter_for_force_constant, double *energy_difference_from_first_structure);
+void Read_en_info2(int *Num_atoms, int *Num_input_structures, double **aray_of_cutoff_distance, double **array_of_mixing_parameters, double *repulsive_sigma, double *repulsive_epsilon, double *fixed_value_of_force_constant, double *energy_parameter_for_force_constant, double *energy_difference_from_first_structure);
+
+void Print_en_input(int Num_atoms, int Num_input_structures, double *aray_of_cutoff_distance, double *array_of_mixing_parameters, double repulsive_sigma, double repulsive_epsilon, double fixed_value_of_force_constant, double energy_parameter_for_force_constant, double energy_difference_from_first_structure);
+void Print_en_input2(int Num_atoms, int Num_input_structures, double *aray_of_cutoff_distance, double *array_of_mixing_parameters, double repulsive_sigma, double repulsive_epsilon, double fixed_value_of_force_constant, double energy_parameter_for_force_constant, double energy_difference_from_first_structure);
+
+void Alloc_en(int Num_atoms, int Num_input_structures, double ****array_of_pair_distance_matrices, double ****array_of_cutoff_matrices, double ***force_constants_all_pairs, double ***sigmas_for_repulsive_part, double ***epsilons_for_repulsive_part, FR_DAT **coordinates_all_structures);
+
+int Read_one_structure(FR_DAT *one_coordinate_set, char filename[1000]);
+
+void Write_one_structure(FR_DAT one_coordinate_set, char filename[1000]);
+
+void Read_input_structures(int Num_input_structures, FR_DAT **coordinates_all_structures);
+void Read_input_structures2(int Num_input_structures, FR_DAT **coordinates_all_structures);
+
+void Calc_simple_distance(int dimension, double *point_1, double *point_2, double *distance, double *distance_squared, double *distance_vector);
+
+void Calc_pair_distances_all_structures(int Num_atoms, int Num_input_structures, FR_DAT *coordinates_all_structures, double ***array_of_pair_distance_matrices);
+
+void Print_pair_distances_all_structures(int Num_atoms, int Num_input_structures, double ***array_of_pair_distance_matrices);
+void Print_pair_distances_all_structures2(int Num_atoms, int Num_input_structures, double ***array_of_pair_distance_matrices);
+
+void Set_various_quantities(int Num_atoms, int Num_input_structures, double ***array_of_cutoff_matrices, double **sigmas_for_repulsive_part, double **epsilons_for_repulsive_part, double *aray_of_cutoff_distances, double repulsive_sigma, double repulsive_epsilon);
+
+double Find_minimum(double number_1, double number_2);
+
+void Set_site_dependent_force_constant_2_state(int Num_input_structures, int Num_atoms, double ***array_of_pair_distance_matrices, double energy_parameter, double fixed_value_of_force_constant, double **force_constants_all_pairs);
+
+void Print_force_constants(int Num_atoms, double **force_constants_all_pairs);
+void Print_force_constants2(int Num_atoms, double **force_constants_all_pairs);
+
+void Cal_repulsive_force_pot_one_pair(double distance, int index_of_site_1, int index_of_site_2, double **sigmas_for_repulsive_part, double **epsilons_for_repulsive_part, int index_of_the_repulsive_function, double *scalar_force, double *potential);
+
+void get_force_one_pair_one_structure(double distance, int index_of_site_1, int index_of_site_2, int index_of_input_structure, double ***array_of_pair_distance_matrices, double **force_constants_all_pairs, double *scalar_force, double *potential);
+
+void getforces(FR_DAT *fr, FR_DAT **coordinates_all_structures, int Num_input_structures, double ***array_of_pair_distance_matrices, double **force_constants_all_pairs, double **sigmas_for_repulsive_part, double **epsilons_for_repulsive_part, double *array_of_mixing_parameters, double *aray_of_cutoff_distances, double energy_difference_from_first_structure);
+
+void getforces_cons(FR_DAT *fr, FR_DAT **coordinates_all_structures, int Num_input_structures, double ***array_of_pair_distance_matrices, double **force_constants_all_pairs, double **sigmas_for_repulsive_part, double **epsilons_for_repulsive_part, double *array_of_mixing_parameters, double *aray_of_cutoff_distances, double energy_difference_from_first_structure, collective_variables *cons_distances, int Num_cv, double KK);
+
+void getforces_cons_harm(FR_DAT *fr, FR_DAT **coordinates_all_structures, int Num_input_structures, double ***array_of_pair_distance_matrices, double **force_constants_all_pairs, double **sigmas_for_repulsive_part, double **epsilons_for_repulsive_part, double *array_of_mixing_parameters, double *aray_of_cutoff_distances, double energy_difference_from_first_structure, collective_variables *cons_distances, int Num_cv, FR_DAT fix_position, double KK, double Kharm);
+
+void getforces_harm(FR_DAT *fr, FR_DAT **coordinates_all_structures, int Num_input_structures, double ***array_of_pair_distance_matrices, double **force_constants_all_pairs, double **sigmas_for_repulsive_part, double **epsilons_for_repulsive_part, double *array_of_mixing_parameters, double *aray_of_cutoff_distances, double energy_difference_from_first_structure, FR_DAT fix_position, double Kharm);
+
+void getforces_cons_harm_omp(FR_DAT *fr, FR_DAT **coordinates_all_structures, int Num_input_structures, double ***array_of_pair_distance_matrices, double **force_constants_all_pairs, double **sigmas_for_repulsive_part, double **epsilons_for_repulsive_part, double *array_of_mixing_parameters, double *aray_of_cutoff_distances, double energy_difference_from_first_structure, collective_variables *cons_distances, int Num_cv, FR_DAT fix_position, double KK, double Kharm, int Num_atoms);
+
+void getforces_harm_omp(FR_DAT *fr, FR_DAT **coordinates_all_structures, int Num_input_structures, double ***array_of_pair_distance_matrices, double **force_constants_all_pairs, double **sigmas_for_repulsive_part, double **epsilons_for_repulsive_part, double *array_of_mixing_parameters, double *aray_of_cutoff_distances, double energy_difference_from_first_structure, FR_DAT fix_position, double Kharm, int Num_atoms);
+#endif
Added: SwiftApps/CMTS/stringmethod/src/force_constants_out
===================================================================
--- SwiftApps/CMTS/stringmethod/src/force_constants_out (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/force_constants_out 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
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+0.751185 2.000000 2.000000 2.000000 1.609064 1.183344 0.529015 0.309158 0.957573 2.000000 1.259759 0.525361 0.385182 0.715390 2.000000 2.000000 2.000000 -1.000000 2.000000 2.000000
+2.000000 2.000000 2.000000 2.000000 2.000000 2.000000 2.000000 1.937719 1.853175 2.000000 2.000000 1.014343 2.000000 1.908640 2.000000 2.000000 2.000000 2.000000 -1.000000 2.000000
+0.941265 2.000000 1.426368 2.000000 2.000000 2.000000 2.000000 2.000000 2.000000 1.031236 0.811317 0.567611 0.941276 0.999337 2.000000 2.000000 2.000000 2.000000 2.000000 -1.000000
Added: SwiftApps/CMTS/stringmethod/src/force_constants_out_2
===================================================================
--- SwiftApps/CMTS/stringmethod/src/force_constants_out_2 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/force_constants_out_2 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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Added: SwiftApps/CMTS/stringmethod/src/include_all.h
===================================================================
--- SwiftApps/CMTS/stringmethod/src/include_all.h (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/include_all.h 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,21 @@
+#ifndef _include_all_h
+#define _include_all_h
+
+#include "calc_rmsd_from_one_structure.h"
+#include "common_functions.h"
+#include "en_boltzmann_mixing_stuff.h"
+#include "integrator_ld_Vanden_Eijnden_Cicotti.h"
+#include "md_ld_common_d_dimension_namd.h"
+#include "output.h"
+#include "perform_langevin_dynamics.h"
+#include "read_configuration.h"
+#include "read_langevin_parameters.h"
+#include "read_masses_all_particles.h"
+#include "read_simulation_parameters.h"
+#include "read_velocities.h"
+#include "write_CA_PDB_files.h"
+#include "write_pdb_atom_record.h"
+#include "write_velocities.h"
+#include "wrtie_configuration.h"
+
+#endif
Added: SwiftApps/CMTS/stringmethod/src/integrator_ld_Vanden_Eijnden_Cicotti.c
===================================================================
--- SwiftApps/CMTS/stringmethod/src/integrator_ld_Vanden_Eijnden_Cicotti.c (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/integrator_ld_Vanden_Eijnden_Cicotti.c 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,166 @@
+/*Written by Avisek Das*/
+/*Last modified on December 19, 2011*/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <string.h>
+#include <time.h>
+
+#include "integrator_ld_Vanden_Eijnden_Cicotti.h"
+
+/*Allocates a strcuture of type 'integrator_langenvin_VE_C'.*/
+void Aolloc_initialize_integration_structure(struct integrator_langenvin_VE_C *Integrator_struct, FR_DAT fr, struct simudetails SimulParam)
+{
+ Integrator_struct->xi = (rvec*)malloc(fr.natoms * sizeof(rvec));
+ Integrator_struct->eta = (rvec*)malloc(fr.natoms * sizeof(rvec));
+ Integrator_struct->A = (rvec*)malloc(fr.natoms * sizeof(rvec));
+
+ double h = SimulParam.timestep;
+ Integrator_struct->h = h;
+ Integrator_struct->h_squared = h * h;
+ Integrator_struct->h_to_three_by_two = sqrt(h * h * h);
+ Integrator_struct->square_root_of_h = sqrt(h);
+
+ Integrator_struct->one_over_two_root_three = 1.0 / (2.0 * sqrt(3));
+}
+
+
+
+/*Generate and store gaussian random numbers*/
+void Generate_and_store_random_numbers(FR_DAT *fr, struct integrator_langenvin_VE_C *Integrator_struct)
+{
+ int i, d, dim;
+
+ dim = DIMENSION;
+
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ for(d = 0 ; d < dim ; d++)
+ {
+ Integrator_struct->xi[i][d] = getnorm();
+ Integrator_struct->eta[i][d] = getnorm();
+ }
+ }
+}
+
+
+
+void Generate_and_store_random_numbers_omp(FR_DAT *fr, struct integrator_langenvin_VE_C *Integrator_struct, struct drand48_data *buffer)
+{
+ int i, d, dim;
+
+ dim = DIMENSION;
+
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ for(d = 0 ; d < dim ; d++)
+ {
+ Integrator_struct->xi[i][d] = getnorm_omp(buffer);
+ Integrator_struct->eta[i][d] = getnorm_omp(buffer);
+
+ //printf("random number %f", Integrator_struct->xi[i][d]);
+ //printf("random number %f", Integrator_struct->eta[i][d]);
+ //printf("\n");
+ }
+ }
+}
+
+
+
+
+/*Calculate accelerations with present forces*/
+void Calc_old_accelerations(FR_DAT *fr, rvec *accelerations_old)
+{
+ int i, d, dim;
+
+ dim = DIMENSION;
+
+ /* calculate current accelerations using current forces*/
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ for(d = 0 ; d < dim ; d++)
+ {
+ accelerations_old[i][d] = fr->f[i][d] / fr->m[i];
+ }
+ }
+}
+
+
+
+/* Calculate A_i 's */
+void Calc_A(FR_DAT *fr, rvec *accelerations_old, struct langevin *Langevin_info, struct integrator_langenvin_VE_C *Integrator_struct)
+{
+ int i, d, dim;
+ double h, h_squared, h_to_three_by_two, one_over_two_root_three;
+
+ dim = DIMENSION;
+
+ h = Integrator_struct->h;
+ h_squared = Integrator_struct->h_squared;
+ h_to_three_by_two = Integrator_struct->h_to_three_by_two;
+ one_over_two_root_three = Integrator_struct->one_over_two_root_three;
+
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ for(d = 0 ; d < dim ; d++)
+ {
+ Integrator_struct->A[i][d] = ( 0.5 * h_squared * ( accelerations_old[i][d]
+ - (Langevin_info->gamma[i] * fr->v[i][d]) ) )
+ + ( Langevin_info->sigma_langevin[i] * h_to_three_by_two * ( (0.5 * Integrator_struct->xi[i][d])
+ + (one_over_two_root_three * Integrator_struct->eta[i][d]) ) );
+ }
+ }
+}
+
+
+
+/*Calculate new positions*/
+void Calc_new_positions(FR_DAT *const fr, struct integrator_langenvin_VE_C *Integrator_struct)
+{
+ int i, d, dim;
+ double h = Integrator_struct->h;
+
+ dim = DIMENSION;
+
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ for(d = 0 ; d < dim ; d++)
+ {
+ fr->x[i][d] = fr->x[i][d] + (h * fr->v[i][d]) + Integrator_struct->A[i][d];
+ }
+ }
+}
+
+
+
+/*Calculate new velocity*/
+void Calc_new_velocities(FR_DAT *const fr, rvec *accelerations_old, rvec *accelerations_new, struct integrator_langenvin_VE_C *Integrator_struct, struct langevin *Langevin_info)
+{
+ int i, d, dim;
+ double h, square_root_of_h;
+
+ dim = DIMENSION;
+ h = Integrator_struct->h;
+ square_root_of_h = Integrator_struct->square_root_of_h;
+
+ /*calculate new accelerations from new forces and then calculate new velocities*/
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ for(d = 0 ; d < dim ; d++)
+ {
+ accelerations_new[i][d] = fr->f[i][d] / fr->m[i];
+ fr->v[i][d] = fr->v[i][d] + (0.5 * h * (accelerations_old[i][d] + accelerations_new[i][d]))
+ - (h * Langevin_info->gamma[i] * fr->v[i][d])
+ + (square_root_of_h * Langevin_info->sigma_langevin[i] * Integrator_struct->xi[i][d])
+ - (Langevin_info->gamma[i] * Integrator_struct->A[i][d]);
+ }
+ }
+
+}
+
+
+
+
+
+
Added: SwiftApps/CMTS/stringmethod/src/integrator_ld_Vanden_Eijnden_Cicotti.h
===================================================================
--- SwiftApps/CMTS/stringmethod/src/integrator_ld_Vanden_Eijnden_Cicotti.h (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/integrator_ld_Vanden_Eijnden_Cicotti.h 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,46 @@
+/*Written by Avisek Das*/
+/*Last modified on September 06, 2011*/
+
+
+#ifndef _integrator_ld_Vanden_Eijnden_Cicotti_h
+#define _integrator_ld_Vanden_Eijnden_Cicotti_h
+
+#include "md_ld_common_d_dimension_namd.h"
+#include "common_functions.h"
+
+
+/* Structure for implementing Langevin dynamics integrator due to Van-Eijnden and Cicotti
+ * for detailed meaning of the symbols see the document 'integrator-langevin.pdf' by Avisek
+ * */
+struct integrator_langenvin_VE_C
+{
+ rvec *xi; /*Array for storing the Gaussian random numbers. xi[i][0]
+ random number of the x component of the i'th particle*/
+ rvec *eta; /*Array of random numbers*/
+ rvec *A; /*This quantity needs to be calcualted for all the particle at
+ every timestep.*/
+ double h; /*timestep*/
+ double h_squared;
+ double h_to_three_by_two; /*h^{3/2}*/
+ double square_root_of_h; /*\sqrt(h)*/
+ double one_over_two_root_three; /*1 / (2 \sqrt(3))*/
+};
+
+
+
+void Aolloc_initialize_integration_structure(struct integrator_langenvin_VE_C *Integrator_struct, FR_DAT fr, struct simudetails SimulParam);
+
+void Generate_and_store_random_numbers(FR_DAT *fr, struct integrator_langenvin_VE_C *Integrator_struct);
+
+void Generate_and_store_random_numbers_omp(FR_DAT *fr, struct integrator_langenvin_VE_C *Integrator_struct, struct drand48_data *buffer);
+
+void Calc_old_accelerations(FR_DAT *fr, rvec *accelerations_old);
+
+void Calc_A(FR_DAT *fr, rvec *accelerations_old, struct langevin *Langevin_info, struct integrator_langenvin_VE_C *Integrator_struct);
+
+void Calc_new_positions(FR_DAT *const fr, struct integrator_langenvin_VE_C *Integrator_struct);
+
+void Calc_new_velocities(FR_DAT *const fr, rvec *accelerations_old, rvec *accelerations_new, struct integrator_langenvin_VE_C *Integrator_struct, struct langevin *Langevin_info);
+
+
+#endif
Added: SwiftApps/CMTS/stringmethod/src/job_omp-stringmethod.sh
===================================================================
--- SwiftApps/CMTS/stringmethod/src/job_omp-stringmethod.sh (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/job_omp-stringmethod.sh 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,7 @@
+#!/bin/bash
+#
+#$ -S /bin/bash -cwd
+#$ -o 1.out -j y
+#$ -pe threaded 4
+
+time ./stringmethod data 350.0
Added: SwiftApps/CMTS/stringmethod/src/kinetic-energies
===================================================================
Added: SwiftApps/CMTS/stringmethod/src/md_ld_common_d_dimension_namd.h
===================================================================
--- SwiftApps/CMTS/stringmethod/src/md_ld_common_d_dimension_namd.h (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/md_ld_common_d_dimension_namd.h 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,197 @@
+/* This file contains common data structures for performing
+ * molecualr dynamics (MD) or Langevin dynamics (LD)
+ * on a multiple component d-dimensional molecular system.
+ No electrostatic interactions, no intramolecular constraints.
+*/
+
+/* To change the dimensionality of the system change the value of DIMENSION.*/
+
+/* These structures can also be used for simple systems like Muller potential.*/
+
+/* For Langevin dynamics we will use the integrator proposed by Vanden-Eijnden and
+ * Ciccotti Chem. Phys. Lett. vol 429, pp 310-316, 2006
+ *
+ * But these structures can presumably be used with other integrators also.*/
+
+/* This structures are analogues of GROMACS strucutres and some structures
+ used by Lanyuan Lu for his force matching program. But some modifications have been used later.*/
+
+/* We change the datatype 'matrix' to 'my_matrix'. Because Numerical Recipes has its own matrix
+ * data type and there was a conflict in namespace while compilation. Pay attention to this
+ * when using this header file for other purposes.*/
+
+/* NAMD units are used. See below*/
+
+/* Units:
+ * Internal
+ * --------
+ * Energy = kcal mol^{-1}
+ * Mass = amu
+ * Distance = \AA (angstrom)
+ * Time = 48.88821291 fs (femto second)
+ *
+ * External
+ * --------
+ * Energy = kcal mol^{-1}
+ * Mass = amu
+ * Distance = \AA (angstrom)
+ * Time = fs (femto second)
+ * */
+
+/* External units are used for all input output for positions and times.
+ * I.e. any quantity that has dimension of length should be in angstrom in both input and output
+ * operations. Similarly for times femtosecond is used for both input and output.
+ * */
+
+/* Unit conversion for qunatities with dimension of time (e.g. timestep) is handled internally.*/
+
+/* IF NEW UNITS ARE INTRODUCED THEN VALUE OF BOLTZMANN CONSTANT SHOULD BE MODIFIED AS WELL AS
+ * UNIT OF TIME SHOULD BE WORKED OUT PROPERLY. THIS MEANS MACROS THAT CONVERT BETWEEN TIME UNITS
+ * (FOR THE PRESENT VERSION THESE ARE 'INTERNAL_TIME_TO_FS' AND 'FS_TO_INTERNAL_TIME') WILL HAVE
+ * DIFFERENT VALUES.*/
+
+/* Written by Avisek Das. */
+
+/* Last modified on December 05, 2011 */
+
+#ifndef _md_ld_common_d_dimension_namd_h
+#define _md_ld_common_d_dimension_namd_h
+
+
+#define VERYSMALL 1.0e-14
+#define VERYSMALL_F 1.0e-6 //small number for single precision
+#define DIMENSION 3 /* Spatial diemnsion.Even though part of
+ this code is flexible to change of
+ dimension, most of it is not. It is
+ strictly applicable for three
+ dimensional systems. */
+#define R2D 57.2957795 //radian to degree conversion factor
+#define D2R 0.0174532925 //degree to radian conversion factor
+/*when energy is in kJ mol^-1, temperature K. These are GROMACS units */
+//#define BOLTZMANN_CONSTANT 0.00831451
+//#define BOLTZMANN_CONSTANT 1.0
+/* when energy is in kcal mol^-1, temperature K. These are NAMD units */
+#define BOLTZMANN_CONSTANT 0.0019872041 // in kcal mol^{-1} K^{-1}
+
+#define INTERNAL_TIME_TO_FS 48.88821291 //conversion factor for internal time unit to femtosecond
+#define FS_TO_INTERNAL_TIME 0.02045482828 //conversion factor from femtosecond to internal time unit
+#define INVERSE_FS_TO_INVERSE_INTERNAL_TIME 48.88821291
+#define INVERSE_INTERNAL_TIME_TO_INVERSE_FS 0.02045482828
+
+
+/* Data types. This is analogous to GROMACS data types.*/
+typedef double my_matrix[DIMENSION][DIMENSION];
+typedef double rvec[DIMENSION];
+
+
+/*Definitions of data structures used*/
+
+
+
+/* This is the data structure for storing the particle coordinates, forces and
+ velocities for one frame (or configuration) of the trajectory. This is the main
+ data structure seen by all funtions in the MD code whenever the functions need
+ coordinate, force or velocity information.*/
+typedef struct
+{
+ int natoms; //total number of atoms
+ my_matrix box; //box dimension
+ double box_dim2[DIMENSION]; //half box length
+
+ rvec *x; /*Coordinates of all the sites.
+ If *fr is the pointer to the data structure
+ for storing the information for one frame.
+ Then
+ x component of position of i th site = fr->x[i][0]
+ y component of position of i th site = fr->x[i][1]
+ z component of position of i th site = fr->x[i][2]
+ Straigtforward generalization for systems with other
+ dimnesions.
+ */
+ rvec *f; /*Total forces on all the atoms.
+ Forces on individual atoms can be accessed in the
+ same manner as the coordinates.
+ */
+ rvec *v; /*Velocities of all the sites.*/
+
+ double *m; /* Masses of the atoms */
+
+ double temperature; /* Temperature of the system*/
+
+ double t; /* time */
+ double E; /* total energy of the system*/
+ double K; /* total kinetic energy of the system*/
+ double U; /* total potential energy of the system*/
+ double U_r; /* energy from the purely replusive part of the potential*/
+ double U_en; /* energy from the elastic net part*/
+ double P; /* pressure */
+
+
+ int ncell; //number of cells
+ int *list; //linked-lists
+ int *head; //head of linked-lists
+ int m0; //number of cells in x-direction
+ int m1; //number of cells in y-direction
+ int m2; //number of cells in z-direction
+ int *map; //neighbor cell map
+ double cellx; //cell dimension in x-direction
+ double celly; //cell dimension in y-direction
+ double cellz; //cell dimension in z-direction
+} FR_DAT;
+
+
+
+/*Simulation details are stored in the structure 'simudetails'*/
+struct simudetails
+{
+ long int RUNLENGTH; /*Total run length in unit of timesteps. */
+ double timestep; /*Timestep used in simulation*/
+ int ColliFreqInTimestep; /*frequency of thermalising collision in
+ the unit of time-steps*/
+ int NumFrames; /*No. of frames for averaging g(r).*/
+ double MaxDistForRDF; /*this is the maximum distance for which
+ g(r) is calculated*/
+ double deltar; /*grid spacing for the distance grid used
+ for g(r) calculation*/
+ long int ConfigSaveFreqTimeStep; /*frequency in the unit of timestep at which
+ configurations are saved to disk.*/
+ long int ProgressFreqTimeStep; /*frequency of wrting progress info*/
+ long int WriteFreqTimestep; /*frequency of writing other stuff to output files*/
+ long int WriteFreqRMSD; /*frequency for writing RMSD to an output file.*/
+ long int WriteFreqPDBtraj; /*frequency for writing configurations to a PDB trajectory file.*/
+};
+
+
+/* Inputs for Langevin dynamics.*/
+struct langevin
+{
+ double *gamma; /*An array with dimension equal to the number of particles
+ in the system that stores the friction coefficients
+ of all the particles. The same value of friction coefficient
+ is used for all the components of a single particle.
+ I.e. for a three dimensional system
+ \gamma_{ix} = \gamma_{ix} = \gamma_{ix} = \gamma_i*/
+
+ double *sigma_langevin; /*An array of length equa to the number of particles in the system with
+ the following values.
+
+ \sigma_i = \sqrt(2 k_B T \gamma_i / m_i)
+
+ where k_B is the Boltzmann constant, m_i is the mass of the i th
+ particle and \gamma_i is the friction coefficient for i th particle.*/
+
+};
+
+typedef struct {
+ int atomi;
+ int atomj;
+ double dis;
+} collective_variables;
+
+typedef struct{
+ rvec *f;
+ double U;
+
+} FR_DAT_MINI;
+
+#endif
Added: SwiftApps/CMTS/stringmethod/src/out_en_boltzmann_mixing_info
===================================================================
--- SwiftApps/CMTS/stringmethod/src/out_en_boltzmann_mixing_info (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/out_en_boltzmann_mixing_info 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,9 @@
+20
+2
+100.000000 100.000000
+0.015000
+2.500000
+1.000000
+2.000000
+5.000000
+0.000000
Added: SwiftApps/CMTS/stringmethod/src/out_en_boltzmann_mixing_info_2
===================================================================
--- SwiftApps/CMTS/stringmethod/src/out_en_boltzmann_mixing_info_2 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/out_en_boltzmann_mixing_info_2 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,9 @@
+38
+2
+100.000000 100.000000
+0.015000
+2.500000
+1.000000
+2.000000
+5.000000
+0.000000
Added: SwiftApps/CMTS/stringmethod/src/output.c
===================================================================
--- SwiftApps/CMTS/stringmethod/src/output.c (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/output.c 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,184 @@
+/*Last modified on November 14, 2011*/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <string.h>
+#include <time.h>
+
+
+#include "output.h"
+
+
+
+
+/*This function opens files for writing energy,KE,PE,pressure at each MD time-step and for tracking progress*/
+int StartFiles(struct simudetails *SimulParam, FILE **energy, FILE **KE, FILE **PE, FILE **pressure)
+{
+ //long int totalsteps = SimulParam->RUNLENGTH;
+ int Num_data_other_output; /* Number of data points in output files. This is
+ determined by 'WRITE_FREQUENCY_OTHER' input in the SIMULPARAMS file*/
+
+ Num_data_other_output = (int)(SimulParam->RUNLENGTH / SimulParam->WriteFreqTimestep);
+
+ *energy = fopen("total-energies", "w");// energy values are stored in a file called "energies.dat"
+ fprintf (*energy, "%d\n", Num_data_other_output);
+ *KE = fopen ("kinetic-energies", "w"); /* kinetic energy values are stored in a file called "kinetic-energies"*/
+ fprintf (*KE, "%d\n", Num_data_other_output);
+ *PE = fopen("potential-energies", "w");/*potential enrgy values are stored in file called "potential-energies"*/
+ fprintf (*PE, "%d\n", Num_data_other_output);
+ //*pressure = fopen("pressures", "w"); /*pressures at each time step are stored in "pressures"*/
+ //fprintf (*pressure, "%lu\n", totalsteps);
+ return 0;
+}
+
+/*This function writes energy, KE, PE, pressure at each time-step to the respective files*/
+int WriteFiles(FR_DAT *fr, FILE *energy, FILE *KE, FILE *PE, FILE *pressure)
+{
+ fprintf (energy, "%.15e\n", fr->E);
+ fprintf (KE, "%.15e\n", fr->K);
+ fprintf (PE, "%.15e\n", fr->U);
+ //fprintf (pressure, "%.15e\n", fr->P);
+ return 0;
+}
+
+
+/*this function is used to calculate the averages and standard deviations of energy, KE, pressure etc at the end of the run. The function takes filename as input
+and open that file to calcualte average and standard deviation. The file should be in the usual format, i.e. first line should have the number of
+entries and then each line should have single entry.*/
+int CalculateAveStdDev(char *Filename, double *Average, double *StandardDeviation)
+{
+ long int NumDataPoints;
+ int i;
+ double FirstDataPoint, DataPoint, SumOfSquares = 0.0, Sum = 0.0, Temp, Mean, MSD;
+ FILE *input;
+ input = fopen(Filename, "r");
+ fscanf (input, " %lu", &NumDataPoints);
+
+ fscanf(input, "%lf", &FirstDataPoint);
+ for(i = 1 ; i < NumDataPoints ; i++)
+ {
+ fscanf(input, "%lf", &DataPoint);
+ Temp = DataPoint - FirstDataPoint;
+ Sum = Sum + Temp;
+ SumOfSquares = SumOfSquares + Temp*Temp;
+ }
+ fclose(input);
+ Mean = (double)(Sum/NumDataPoints);
+ MSD = (double)(SumOfSquares/NumDataPoints) - Mean*Mean;
+ *StandardDeviation = sqrt(MSD);
+ *Average = Mean + FirstDataPoint;
+ return 0;
+}
+
+
+
+/*wirites the summary of the calculation performed in a file called 'summary'*/
+int WriteSummary(struct simudetails *SimulParam, FR_DAT *fr, double temperature, double Average_kinetic_enenrgy)
+{
+ //int d;
+ int dim = DIMENSION;
+ FILE *rite;
+ rite = fopen("summary", "w");
+ fprintf(rite, "SUMMARY OF MOLECULAR DYNAMICS / LANGEVIN DYNAMICS SIMULATION PERFORMED\n");
+ fprintf(rite, "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\n");
+ fprintf(rite, "Number of particles: %d\n", fr->natoms);
+ /*fprintf(rite, "Box Length: ");
+ for(d = 0 ; d < dim ; d++)
+ {
+ fprintf(rite, "%lf ", fr->box[d][d]);
+ }
+ fprintf(rite, "\n");*/
+ fprintf(rite, "Temperature: %lf K\n", temperature);
+
+ fprintf(rite, "\nDetails of Simulation Parameters\n");
+ fprintf(rite, "--------------------------------\n");
+ fprintf(rite, "Runlength in the unit of time-steps: %lu\n", SimulParam->RUNLENGTH);
+ fprintf(rite, "Runlength in the unit of time: %.15e fs\n", ( ((double)(SimulParam->RUNLENGTH))*(SimulParam->timestep) * INTERNAL_TIME_TO_FS));
+ fprintf(rite, "Timestep: %.15e internal unit\n", SimulParam->timestep);
+ fprintf(rite, "Timestep: %.15e fs\n", (SimulParam->timestep * INTERNAL_TIME_TO_FS));
+ //fprintf(rite, "Collision frequency in unit of time-steps: %d\n", SimulParam->ColliFreqInTimestep);
+
+
+
+ /*calculates some average quantities*/
+ //double avePressure, aveTotalEnergy, aveKE, avePE;
+ //double stddevPressure, stddevTotalEnergy, stddevKE, stddevPE;
+ double aveTotalEnergy, aveKE, avePE;
+ double stddevTotalEnergy, stddevKE, stddevPE;
+ char filename[256];
+
+ //sprintf(filename, "pressures");
+ //CalculateAveStdDev(filename, &avePressure, &stddevPressure);
+
+ sprintf(filename, "total-energies");
+ CalculateAveStdDev(filename, &aveTotalEnergy, &stddevTotalEnergy);
+
+ sprintf(filename, "kinetic-energies");
+ CalculateAveStdDev(filename, &aveKE, &stddevKE);
+
+ sprintf(filename, "potential-energies");
+ CalculateAveStdDev(filename, &avePE, &stddevPE);
+
+ fprintf(rite, "\nAverages and Standard Deviations of various quantities from output files\n");
+ fprintf(rite, "-------------------------------------------------------\n");
+
+ //fprintf(rite, "Average Pressure: %lf Standard Deviation of Pressure: %lf\n", avePressure, stddevPressure);
+ fprintf(rite, "Average Total Energy: %.15e Standard Deviation of Total Energy: %.15e\n", aveTotalEnergy, stddevTotalEnergy);
+ fprintf(rite, "Average Kinetic Energy: %lf Standard Deviation of Kinetic Energy: %lf\n", aveKE, stddevKE);
+ fprintf(rite, "Average Potential Energy Particles: %lf Standard Deviation of Potential Energy: %lf\n", avePE, stddevPE);
+
+
+ fprintf(rite, "\nTemperature control\n");
+ fprintf(rite, "-----------------------\n");
+ double ParticleTemperature;
+ double k_b = BOLTZMANN_CONSTANT; /*Boltzmann constant*/
+ //ParticleTemperature = (2.00 * aveKE) / ((3.00 * fr->natoms - 3) * k_b); /*we subtract the center of mass motion. Hence the actual no. of degrees of freedom = 3N-3 in 3 dimension.*/
+ aveKE = Average_kinetic_enenrgy; //This is the actual value for the entire run
+ /*Special case for one particle system*/
+ if(fr->natoms == 1)
+ {
+ ParticleTemperature = (2.00 * aveKE) / (dim * k_b);
+ }
+ else
+ {
+ ParticleTemperature = (2.00 * aveKE) / (dim * (fr->natoms - 1) * k_b);
+ }
+ fprintf(rite, "Actual value of average kinetic energy: %.15e\n", aveKE);
+ fprintf(rite, "Observed temperature for particles: %lf K\n", ParticleTemperature);
+ fprintf(rite, "Value of Boltzmann constant used: %.15e\n", k_b);
+
+
+ fclose(rite);
+ return 0;
+}
+
+
+
+void Write_masses(FR_DAT *fr)
+{
+ int i;
+ FILE *rite1;
+
+ rite1 = fopen("masses_out", "w");
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ fprintf(rite1, "%lf\n", fr->m[i]);
+ }
+ fclose(rite1);
+}
+
+
+void Write_friction_coefficients(FR_DAT *fr, struct langevin Langevin_info)
+{
+ int i;
+ FILE *rite1;
+ rite1 = fopen("friction_out", "w");
+ fprintf(rite1, "Friction coefficients are in the unit of (internal time unit)^{-1}\n");
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ fprintf(rite1, "%lf\n", Langevin_info.gamma[i]);
+ }
+ fclose(rite1);
+}
+
Added: SwiftApps/CMTS/stringmethod/src/output.h
===================================================================
--- SwiftApps/CMTS/stringmethod/src/output.h (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/output.h 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,22 @@
+#ifndef _output_h
+#define _output_h
+
+#include "md_ld_common_d_dimension_namd.h"
+
+
+int StartFiles(struct simudetails *SimulParam, FILE **energy, FILE **KE, FILE **PE, FILE **pressure);
+
+
+int WriteFiles(FR_DAT *fr, FILE *energy, FILE *KE, FILE *PE, FILE *pressure);
+
+
+int CalculateAveStdDev(char *Filename, double *Average, double *StandardDeviation);
+
+int WriteSummary(struct simudetails *SimulParam, FR_DAT *fr, double temperature, double Average_kinetic_enenrgy);
+
+void Write_masses(FR_DAT *fr);
+
+void Write_friction_coefficients(FR_DAT *fr, struct langevin Langevin_info);
+
+
+#endif
Added: SwiftApps/CMTS/stringmethod/src/pair_distances_1
===================================================================
--- SwiftApps/CMTS/stringmethod/src/pair_distances_1 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/pair_distances_1 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
+-1.000000 3.778030 5.728746 9.102461 11.209872 14.499611 15.454605 12.572499 10.140000 7.099642 5.940073 4.754316 6.503213 7.213845 10.100782 10.101963 8.930094 9.901207 11.197765 13.024046
+3.778030 -1.000000 3.800891 6.095633 9.065608 11.808240 12.956701 10.707574 7.680071 5.758737 4.621703 6.092269 7.888525 10.006437 12.558519 11.446241 9.981606 9.459946 10.280562 11.052589
+5.728746 3.800891 -1.000000 3.798258 5.589228 8.859748 10.348338 8.087778 6.081176 5.025371 6.488800 8.121391 10.938505 12.499164 14.665699 13.710687 11.330739 10.770706 10.240888 10.535469
+9.102461 6.095633 3.798258 -1.000000 3.804071 5.740425 7.334878 6.227608 4.037336 5.637654 7.547453 10.423011 13.148755 15.374788 17.181298 15.500198 12.942759 11.278464 9.994659 8.893369
+11.209872 9.065608 5.589228 3.804071 -1.000000 3.798471 5.932115 5.064575 5.549442 7.387487 10.389057 12.705926 15.916519 17.585804 19.167475 17.829610 14.789243 13.507319 11.402247 10.245949
+14.499611 11.808240 8.859748 5.740425 3.798471 -1.000000 3.784668 5.661594 6.665755 9.798681 12.620076 15.519158 18.568575 20.668229 22.057382 20.245264 17.204049 15.233259 12.733563 10.473561
+15.454605 12.956701 10.348338 7.334878 5.932115 3.784668 -1.000000 3.809079 5.898284 9.332664 12.379835 15.326968 18.514600 20.696771 21.450492 19.307960 16.058293 13.783593 10.695733 8.014233
+12.572499 10.707574 8.087778 6.227608 5.064575 5.661594 3.809079 -1.000000 3.782016 6.185617 9.696392 12.130342 15.582022 17.406303 18.004132 16.139181 12.704078 10.955224 7.837492 6.327776
+10.140000 7.680071 6.081176 4.037336 5.549442 6.665755 5.898284 3.782016 -1.000000 3.776242 6.483022 9.577024 12.629130 14.980662 15.916013 13.743847 10.768292 8.570046 6.413451 4.979832
+7.099642 5.758737 5.025371 5.637654 7.387487 9.798681 9.332664 6.185617 3.776242 -1.000000 3.792257 6.010292 9.416019 11.368420 12.313002 10.538757 7.508864 6.306434 5.226952 6.253876
+5.940073 4.621703 6.488800 7.547453 10.389057 12.620076 12.379835 9.696392 6.483022 3.792257 -1.000000 3.801052 6.184198 8.976172 10.239096 8.068563 6.195598 4.862542 6.222697 7.734118
+4.754316 6.092269 8.121391 10.423011 12.705926 15.519158 15.326968 12.130342 9.577024 6.010292 3.801052 -1.000000 3.802379 5.432243 6.791227 5.700341 4.317113 5.652049 7.859623 10.556256
+6.503213 7.888525 10.938505 13.148755 15.916519 18.568575 18.514600 15.582022 12.629130 9.416019 6.184198 3.802379 -1.000000 3.813821 5.784760 4.798891 6.123177 7.411318 10.628658 13.183906
+7.213845 10.006437 12.499164 15.374788 17.585804 20.668229 20.696771 17.406303 14.980662 11.368420 8.976172 5.432243 3.813821 -1.000000 3.786264 5.656963 7.102229 9.831364 12.705339 15.754329
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Added: SwiftApps/CMTS/stringmethod/src/pair_distances_2
===================================================================
--- SwiftApps/CMTS/stringmethod/src/pair_distances_2 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/pair_distances_2 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,20 @@
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Added: SwiftApps/CMTS/stringmethod/src/pair_distances_2_1
===================================================================
--- SwiftApps/CMTS/stringmethod/src/pair_distances_2_1 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/pair_distances_2_1 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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Added: SwiftApps/CMTS/stringmethod/src/pair_distances_2_2
===================================================================
--- SwiftApps/CMTS/stringmethod/src/pair_distances_2_2 (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/pair_distances_2_2 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,38 @@
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+15.328823 16.485711 12.437520 12.099951 12.407742 13.452155 10.472106 10.236385 11.557278 11.852236 10.977205 7.564049 7.651381 5.729729 6.657184 5.820510 5.281403 8.455819 9.662426 10.216621 9.719905 13.524226 14.124373 15.488670 14.806692 17.991138 15.593886 15.465708 12.573947 12.761241 9.421268 9.232341 6.781473 7.267361 3.687243 4.184439 -1.000000 1.549099
+16.668790 17.860058 13.880682 13.538579 13.933517 14.953700 12.006881 11.764342 12.957476 13.217288 12.185891 8.610292 8.485854 6.955310 7.745297 7.354873 6.819191 9.832681 11.021666 11.436072 10.849804 14.703774 15.369681 16.507706 15.765673 18.920134 16.369522 16.118906 13.519429 13.739651 10.173083 9.938610 7.510675 7.854874 4.651738 5.277782 1.549099 -1.000000
Added: SwiftApps/CMTS/stringmethod/src/perform_langevin_dynamics.c
===================================================================
--- SwiftApps/CMTS/stringmethod/src/perform_langevin_dynamics.c (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/perform_langevin_dynamics.c 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,404 @@
+/* Main loop for Langevin dynamics simulation*/
+
+/* Last modified on December 19, 2011*/
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <time.h>
+#include <string.h>
+
+#include "perform_langevin_dynamics.h"
+
+void Perform_langevin_dynamics(FR_DAT *fr, struct simudetails *SimulParam, struct langevin *Langevin_info, rvec *accelerations_old, rvec *accelerations_new, struct integrator_langenvin_VE_C *Integrator_struct, FR_DAT **coordinates_all_structures, int Num_input_structures, double ***array_of_pair_distance_matrices, double **force_constants_all_pairs, double **sigmas_for_repulsive_part, double **epsilons_for_repulsive_part, double *array_of_mixing_parameters, double *aray_of_cutoff_distances, double energy_difference_from_first_structure, double *Average_kinetic_enenrgy)
+{
+ long int q;
+ long int config_index;
+
+ double rmsd_from_structure_1, rmsd_from_structure_2, time_in_fs;
+
+ /* main MD/LD loop*/
+ for(q = 0; q < SimulParam->RUNLENGTH; q++)
+ {
+ /** Writes structure related output files **/
+ /* saves configuration to trajectory file*/
+ /* if(q % SimulParam->ConfigSaveFreqTimeStep == 0)
+ {
+ Write_config_to_trajectory_file_only_coordinates(fr, trajectory);
+ } */
+ /* Write RMSD*/
+ /* if((q % SimulParam->WriteFreqRMSD) == 0)
+ {
+ time_in_fs = fr->t * INTERNAL_TIME_TO_FS;
+ rmsd_from_structure_1 = Calc_rmsd(fr, &(*coordinates_all_structures)[0]);
+ rmsd_from_structure_2 = Calc_rmsd(fr, &(*coordinates_all_structures)[1]);
+ fprintf(rmsd_1, "%.8e %.15e\n", time_in_fs, rmsd_from_structure_1);
+ fprintf(rmsd_2, "%.8e %.15e\n", time_in_fs, rmsd_from_structure_2);
+ } */
+ /* Write config to PDB trajectory file*/
+ /* if((q % SimulParam->WriteFreqPDBtraj) == 0)
+ {
+ config_index = (long int)(q / SimulParam->WriteFreqPDBtraj) + 1;
+ Write_config_to_a_PDB_trajectory_file_1(pdb_traj, fr, Residue_names, config_index);
+ } */
+ /** End of writing structure related output files **/
+
+ /* Calcualte total energy*/
+ get_kinetic_energy(fr);
+ fr->E = fr->U + fr->K;
+
+ /* Writes various quantites to files*/
+ // if((q % SimulParam->WriteFreqTimestep) == 0)
+ // {
+ // WriteFiles(fr, energy, KE, PE, pressure);
+ /*Wrtie two contribution to potential energy*/
+ // fprintf(out_r, "%.15e\n", fr->U_r);
+ // fprintf(out_en, "%.15e\n", fr->U_en);
+ // }
+ /* Prints updates at regular interval*/
+ /* if ((q % SimulParam->ProgressFreqTimeStep) == 0)
+ {
+ fprintf (progress, "%g %lu %g %g %g\n", (fr->t * INTERNAL_TIME_TO_FS), q, fr->U, fr->K, fr->E);
+ fflush(progress);
+ }
+*/
+ /*Sum total kinetic eenrgy*/
+ *Average_kinetic_enenrgy = *Average_kinetic_enenrgy + fr->K;
+
+ /** Perform integration using Vanden-Eijnden Cicotti integrator **/
+ /* Generate random numbers*/
+ Generate_and_store_random_numbers(fr, Integrator_struct);
+ /* Calculate old accelerations*/
+ Calc_old_accelerations(fr, accelerations_old);
+ /*Calculate the A vectors*/
+ Calc_A(fr, accelerations_old, Langevin_info, Integrator_struct);
+ /* Calculate new positions */
+ Calc_new_positions(fr, Integrator_struct);
+ /* Calculates new forces using new positions. Also calculate the new potential energy*/
+ getforces(fr, coordinates_all_structures, Num_input_structures, array_of_pair_distance_matrices, force_constants_all_pairs, sigmas_for_repulsive_part, epsilons_for_repulsive_part, array_of_mixing_parameters, aray_of_cutoff_distances, energy_difference_from_first_structure);
+ /* Calculate new velocities*/
+ Calc_new_velocities(fr, accelerations_old, accelerations_new, Integrator_struct, Langevin_info);
+ /*removes the drift*/
+ velocenter(fr);
+
+ /* Increase the time*/
+ fr->t = fr->t + SimulParam->timestep;
+ }
+}
+
+
+void Perform_langevin_dynamics_cons(FR_DAT *fr, struct simudetails *SimulParam, struct langevin *Langevin_info, rvec *accelerations_old, rvec *accelerations_new, struct integrator_langenvin_VE_C *Integrator_struct, FR_DAT **coordinates_all_structures, int Num_input_structures, double ***array_of_pair_distance_matrices, double **force_constants_all_pairs, double **sigmas_for_repulsive_part, double **epsilons_for_repulsive_part, double *array_of_mixing_parameters, double *aray_of_cutoff_distances, double energy_difference_from_first_structure, double *Average_kinetic_enenrgy, collective_variables *cons_distances, int Num_cv, double KK)
+{
+ long int q;
+ long int config_index;
+
+ double rmsd_from_structure_1, rmsd_from_structure_2, time_in_fs;
+
+ /* main MD/LD loop*/
+ for(q = 0; q < SimulParam->RUNLENGTH; q++)
+ {
+ /** Writes structure related output files **/
+ /* saves configuration to trajectory file*/
+ /* if(q % SimulParam->ConfigSaveFreqTimeStep == 0)
+ {
+ Write_config_to_trajectory_file_only_coordinates(fr, trajectory);
+ } */
+ /* Write RMSD*/
+ /* if((q % SimulParam->WriteFreqRMSD) == 0)
+ {
+ time_in_fs = fr->t * INTERNAL_TIME_TO_FS;
+ rmsd_from_structure_1 = Calc_rmsd(fr, &(*coordinates_all_structures)[0]);
+ rmsd_from_structure_2 = Calc_rmsd(fr, &(*coordinates_all_structures)[1]);
+ fprintf(rmsd_1, "%.8e %.15e\n", time_in_fs, rmsd_from_structure_1);
+ fprintf(rmsd_2, "%.8e %.15e\n", time_in_fs, rmsd_from_structure_2);
+ } */
+ /* Write config to PDB trajectory file*/
+ /* if((q % SimulParam->WriteFreqPDBtraj) == 0)
+ {
+ config_index = (long int)(q / SimulParam->WriteFreqPDBtraj) + 1;
+ Write_config_to_a_PDB_trajectory_file_1(pdb_traj, fr, Residue_names, config_index);
+ } */
+ /** End of writing structure related output files **/
+
+ /* Calcualte total energy*/
+ get_kinetic_energy(fr);
+ fr->E = fr->U + fr->K;
+
+ /* Writes various quantites to files*/
+ // if((q % SimulParam->WriteFreqTimestep) == 0)
+ // {
+ // WriteFiles(fr, energy, KE, PE, pressure);
+ /*Wrtie two contribution to potential energy*/
+ // fprintf(out_r, "%.15e\n", fr->U_r);
+ // fprintf(out_en, "%.15e\n", fr->U_en);
+ // }
+ /* Prints updates at regular interval*/
+ /* if ((q % SimulParam->ProgressFreqTimeStep) == 0)
+ {
+ fprintf (progress, "%g %lu %g %g %g\n", (fr->t * INTERNAL_TIME_TO_FS), q, fr->U, fr->K, fr->E);
+ fflush(progress);
+ }
+*/
+ /*Sum total kinetic eenrgy*/
+ *Average_kinetic_enenrgy = *Average_kinetic_enenrgy + fr->K;
+
+ /** Perform integration using Vanden-Eijnden Cicotti integrator **/
+ /* Generate random numbers*/
+ Generate_and_store_random_numbers(fr, Integrator_struct);
+ /* Calculate old accelerations*/
+ Calc_old_accelerations(fr, accelerations_old);
+ /*Calculate the A vectors*/
+ Calc_A(fr, accelerations_old, Langevin_info, Integrator_struct);
+ /* Calculate new positions */
+ Calc_new_positions(fr, Integrator_struct);
+ /* Calculates new forces using new positions. Also calculate the new potential energy*/
+ getforces_cons(fr, coordinates_all_structures, Num_input_structures, array_of_pair_distance_matrices, force_constants_all_pairs, sigmas_for_repulsive_part, epsilons_for_repulsive_part, array_of_mixing_parameters, aray_of_cutoff_distances, energy_difference_from_first_structure, cons_distances, Num_cv, KK);
+ /* Calculate new velocities*/
+ Calc_new_velocities(fr, accelerations_old, accelerations_new, Integrator_struct, Langevin_info);
+ /*removes the drift*/
+ velocenter(fr);
+
+ /* Increase the time*/
+ fr->t = fr->t + SimulParam->timestep;
+ }
+}
+
+
+
+void Perform_langevin_dynamics_cons_harm(FR_DAT *fr, struct simudetails *SimulParam, struct langevin *Langevin_info, rvec *accelerations_old, rvec *accelerations_new, struct integrator_langenvin_VE_C *Integrator_struct, FR_DAT **coordinates_all_structures, int Num_input_structures, double ***array_of_pair_distance_matrices, double **force_constants_all_pairs, double **sigmas_for_repulsive_part, double **epsilons_for_repulsive_part, double *array_of_mixing_parameters, double *aray_of_cutoff_distances, double energy_difference_from_first_structure, double *Average_kinetic_enenrgy, collective_variables *cons_distances, int Num_cv, FR_DAT fix_position, double KK, double Kharm)
+{
+ long int q;
+ long int config_index;
+
+ double rmsd_from_structure_1, rmsd_from_structure_2, time_in_fs;
+
+ /* main MD/LD loop*/
+ for(q = 0; q < SimulParam->RUNLENGTH; q++)
+ {
+ /** Writes structure related output files **/
+ /* saves configuration to trajectory file*/
+ /* if(q % SimulParam->ConfigSaveFreqTimeStep == 0)
+ {
+ Write_config_to_trajectory_file_only_coordinates(fr, trajectory);
+ } */
+ /* Write RMSD*/
+ /* if((q % SimulParam->WriteFreqRMSD) == 0)
+ {
+ time_in_fs = fr->t * INTERNAL_TIME_TO_FS;
+ rmsd_from_structure_1 = Calc_rmsd(fr, &(*coordinates_all_structures)[0]);
+ rmsd_from_structure_2 = Calc_rmsd(fr, &(*coordinates_all_structures)[1]);
+ fprintf(rmsd_1, "%.8e %.15e\n", time_in_fs, rmsd_from_structure_1);
+ fprintf(rmsd_2, "%.8e %.15e\n", time_in_fs, rmsd_from_structure_2);
+ } */
+ /* Write config to PDB trajectory file*/
+ /* if((q % SimulParam->WriteFreqPDBtraj) == 0)
+ {
+ config_index = (long int)(q / SimulParam->WriteFreqPDBtraj) + 1;
+ Write_config_to_a_PDB_trajectory_file_1(pdb_traj, fr, Residue_names, config_index);
+ } */
+ /** End of writing structure related output files **/
+
+ /* Calcualte total energy*/
+ get_kinetic_energy(fr);
+ fr->E = fr->U + fr->K;
+
+ /* Writes various quantites to files*/
+ // if((q % SimulParam->WriteFreqTimestep) == 0)
+ // {
+ // WriteFiles(fr, energy, KE, PE, pressure);
+ /*Wrtie two contribution to potential energy*/
+ // fprintf(out_r, "%.15e\n", fr->U_r);
+ // fprintf(out_en, "%.15e\n", fr->U_en);
+ // }
+ /* Prints updates at regular interval*/
+ /* if ((q % SimulParam->ProgressFreqTimeStep) == 0)
+ {
+ fprintf (progress, "%g %lu %g %g %g\n", (fr->t * INTERNAL_TIME_TO_FS), q, fr->U, fr->K, fr->E);
+ fflush(progress);
+ }
+*/
+ /*Sum total kinetic eenrgy*/
+ *Average_kinetic_enenrgy = *Average_kinetic_enenrgy + fr->K;
+
+ /** Perform integration using Vanden-Eijnden Cicotti integrator **/
+ /* Generate random numbers*/
+ Generate_and_store_random_numbers(fr, Integrator_struct);
+ /* Calculate old accelerations*/
+ Calc_old_accelerations(fr, accelerations_old);
+ /*Calculate the A vectors*/
+ Calc_A(fr, accelerations_old, Langevin_info, Integrator_struct);
+ /* Calculate new positions */
+ Calc_new_positions(fr, Integrator_struct);
+ /* Calculates new forces using new positions. Also calculate the new potential energy*/
+ getforces_cons_harm(fr, coordinates_all_structures, Num_input_structures, array_of_pair_distance_matrices, force_constants_all_pairs, sigmas_for_repulsive_part, epsilons_for_repulsive_part, array_of_mixing_parameters, aray_of_cutoff_distances, energy_difference_from_first_structure, cons_distances, Num_cv, fix_position, KK, Kharm);
+ /* Calculate new velocities*/
+ Calc_new_velocities(fr, accelerations_old, accelerations_new, Integrator_struct, Langevin_info);
+ /*removes the drift*/
+ velocenter(fr);
+
+ /* Increase the time*/
+ fr->t = fr->t + SimulParam->timestep;
+ }
+}
+
+
+
+void Perform_langevin_dynamics_harm(FR_DAT *fr, struct simudetails *SimulParam, struct langevin *Langevin_info, rvec *accelerations_old, rvec *accelerations_new, struct integrator_langenvin_VE_C *Integrator_struct, FR_DAT **coordinates_all_structures, int Num_input_structures, double ***array_of_pair_distance_matrices, double **force_constants_all_pairs, double **sigmas_for_repulsive_part, double **epsilons_for_repulsive_part, double *array_of_mixing_parameters, double *aray_of_cutoff_distances, double energy_difference_from_first_structure, double *Average_kinetic_enenrgy, FR_DAT fix_position, double Kharm)
+{
+ long int q;
+ long int config_index;
+
+ double rmsd_from_structure_1, rmsd_from_structure_2, time_in_fs;
+
+ /* main MD/LD loop*/
+ for(q = 0; q < SimulParam->RUNLENGTH; q++)
+ {
+ /** Writes structure related output files **/
+ /* saves configuration to trajectory file*/
+ /* if(q % SimulParam->ConfigSaveFreqTimeStep == 0)
+ {
+ Write_config_to_trajectory_file_only_coordinates(fr, trajectory);
+ } */
+ /* Write RMSD*/
+ /* if((q % SimulParam->WriteFreqRMSD) == 0)
+ {
+ time_in_fs = fr->t * INTERNAL_TIME_TO_FS;
+ rmsd_from_structure_1 = Calc_rmsd(fr, &(*coordinates_all_structures)[0]);
+ rmsd_from_structure_2 = Calc_rmsd(fr, &(*coordinates_all_structures)[1]);
+ fprintf(rmsd_1, "%.8e %.15e\n", time_in_fs, rmsd_from_structure_1);
+ fprintf(rmsd_2, "%.8e %.15e\n", time_in_fs, rmsd_from_structure_2);
+ } */
+ /* Write config to PDB trajectory file*/
+ /* if((q % SimulParam->WriteFreqPDBtraj) == 0)
+ {
+ config_index = (long int)(q / SimulParam->WriteFreqPDBtraj) + 1;
+ Write_config_to_a_PDB_trajectory_file_1(pdb_traj, fr, Residue_names, config_index);
+ } */
+ /** End of writing structure related output files **/
+
+ /* Calcualte total energy*/
+ get_kinetic_energy(fr);
+ fr->E = fr->U + fr->K;
+
+ /* Writes various quantites to files*/
+ // if((q % SimulParam->WriteFreqTimestep) == 0)
+ // {
+ // WriteFiles(fr, energy, KE, PE, pressure);
+ /*Wrtie two contribution to potential energy*/
+ // fprintf(out_r, "%.15e\n", fr->U_r);
+ // fprintf(out_en, "%.15e\n", fr->U_en);
+ // }
+ /* Prints updates at regular interval*/
+ /* if ((q % SimulParam->ProgressFreqTimeStep) == 0)
+ {
+ fprintf (progress, "%g %lu %g %g %g\n", (fr->t * INTERNAL_TIME_TO_FS), q, fr->U, fr->K, fr->E);
+ fflush(progress);
+ }
+*/
+ /*Sum total kinetic eenrgy*/
+ *Average_kinetic_enenrgy = *Average_kinetic_enenrgy + fr->K;
+
+ /** Perform integration using Vanden-Eijnden Cicotti integrator **/
+ /* Generate random numbers*/
+ Generate_and_store_random_numbers(fr, Integrator_struct);
+ /* Calculate old accelerations*/
+ Calc_old_accelerations(fr, accelerations_old);
+ /*Calculate the A vectors*/
+ Calc_A(fr, accelerations_old, Langevin_info, Integrator_struct);
+ /* Calculate new positions */
+ Calc_new_positions(fr, Integrator_struct);
+ /* Calculates new forces using new positions. Also calculate the new potential energy*/
+ getforces_harm(fr, coordinates_all_structures, Num_input_structures, array_of_pair_distance_matrices, force_constants_all_pairs, sigmas_for_repulsive_part, epsilons_for_repulsive_part, array_of_mixing_parameters, aray_of_cutoff_distances, energy_difference_from_first_structure, fix_position, Kharm);
+ /* Calculate new velocities*/
+ Calc_new_velocities(fr, accelerations_old, accelerations_new, Integrator_struct, Langevin_info);
+ /*removes the drift*/
+ velocenter(fr);
+
+ /* Increase the time*/
+ fr->t = fr->t + SimulParam->timestep;
+ }
+}
+
+
+void Perform_langevin_dynamics_harm_omp(FR_DAT *fr, struct simudetails *SimulParam, struct langevin *Langevin_info, rvec *accelerations_old, rvec *accelerations_new, struct integrator_langenvin_VE_C *Integrator_struct, FR_DAT **coordinates_all_structures, int Num_input_structures, double ***array_of_pair_distance_matrices, double **force_constants_all_pairs, double **sigmas_for_repulsive_part, double **epsilons_for_repulsive_part, double *array_of_mixing_parameters, double *aray_of_cutoff_distances, double energy_difference_from_first_structure, double *Average_kinetic_enenrgy, FR_DAT fix_position, double Kharm, int Num_atoms, struct drand48_data *buffer)
+{
+ long int q;
+ long int config_index;
+
+ double rmsd_from_structure_1, rmsd_from_structure_2, time_in_fs;
+
+ /* main MD/LD loop*/
+ for(q = 0; q < SimulParam->RUNLENGTH; q++)
+ {
+
+ /* Calcualte total energy*/
+ get_kinetic_energy(fr);
+ fr->E = fr->U + fr->K;
+
+ /*Sum total kinetic eenrgy*/
+ *Average_kinetic_enenrgy = *Average_kinetic_enenrgy + fr->K;
+
+ /** Perform integration using Vanden-Eijnden Cicotti integrator **/
+ /* Generate random numbers*/
+ Generate_and_store_random_numbers_omp(fr, Integrator_struct, buffer);
+ /* Calculate old accelerations*/
+ Calc_old_accelerations(fr, accelerations_old);
+ /*Calculate the A vectors*/
+ Calc_A(fr, accelerations_old, Langevin_info, Integrator_struct);
+ /* Calculate new positions */
+ Calc_new_positions(fr, Integrator_struct);
+ /* Calculates new forces using new positions. Also calculate the new potential energy*/
+ getforces_harm_omp(fr, coordinates_all_structures, Num_input_structures, array_of_pair_distance_matrices, force_constants_all_pairs, sigmas_for_repulsive_part, epsilons_for_repulsive_part, array_of_mixing_parameters, aray_of_cutoff_distances, energy_difference_from_first_structure, fix_position, Kharm, Num_atoms);
+ /* Calculate new velocities*/
+ Calc_new_velocities(fr, accelerations_old, accelerations_new, Integrator_struct, Langevin_info);
+ /*removes the drift*/
+ velocenter(fr);
+
+ /* Increase the time*/
+ fr->t = fr->t + SimulParam->timestep;
+ }
+}
+
+
+void Perform_langevin_dynamics_cons_harm_omp(FR_DAT *fr, struct simudetails *SimulParam, struct langevin *Langevin_info, rvec *accelerations_old, rvec *accelerations_new, struct integrator_langenvin_VE_C *Integrator_struct, FR_DAT **coordinates_all_structures, int Num_input_structures, double ***array_of_pair_distance_matrices, double **force_constants_all_pairs, double **sigmas_for_repulsive_part, double **epsilons_for_repulsive_part, double *array_of_mixing_parameters, double *aray_of_cutoff_distances, double energy_difference_from_first_structure, double *Average_kinetic_enenrgy, collective_variables *cons_distances, int Num_cv, FR_DAT fix_position, double KK, double Kharm, int Num_atoms, struct drand48_data *buffer)
+{
+ long int q;
+ long int config_index;
+
+ double rmsd_from_structure_1, rmsd_from_structure_2, time_in_fs;
+
+ /* main MD/LD loop*/
+ for(q = 0; q < SimulParam->RUNLENGTH; q++)
+ {
+
+ /* Calcualte total energy*/
+ get_kinetic_energy(fr);
+ fr->E = fr->U + fr->K;
+
+ /*Sum total kinetic eenrgy*/
+ *Average_kinetic_enenrgy = *Average_kinetic_enenrgy + fr->K;
+
+ /** Perform integration using Vanden-Eijnden Cicotti integrator **/
+ /* Generate random numbers*/
+ Generate_and_store_random_numbers_omp(fr, Integrator_struct, buffer);
+ /* Calculate old accelerations*/
+ Calc_old_accelerations(fr, accelerations_old);
+ /*Calculate the A vectors*/
+ Calc_A(fr, accelerations_old, Langevin_info, Integrator_struct);
+ /* Calculate new positions */
+ Calc_new_positions(fr, Integrator_struct);
+ /* Calculates new forces using new positions. Also calculate the new potential energy*/
+ getforces_cons_harm_omp(fr, coordinates_all_structures, Num_input_structures, array_of_pair_distance_matrices, force_constants_all_pairs, sigmas_for_repulsive_part, epsilons_for_repulsive_part, array_of_mixing_parameters, aray_of_cutoff_distances, energy_difference_from_first_structure, cons_distances, Num_cv, fix_position, KK, Kharm, Num_atoms);
+ /* Calculate new velocities*/
+ Calc_new_velocities(fr, accelerations_old, accelerations_new, Integrator_struct, Langevin_info);
+ /*removes the drift*/
+ velocenter(fr);
+
+ /* Increase the time*/
+ fr->t = fr->t + SimulParam->timestep;
+ }
+}
+
+
+
Added: SwiftApps/CMTS/stringmethod/src/perform_langevin_dynamics.h
===================================================================
--- SwiftApps/CMTS/stringmethod/src/perform_langevin_dynamics.h (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/perform_langevin_dynamics.h 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,26 @@
+#ifndef _perform_langevin_dynamics_h
+#define _perform_langevin_dynamics_h
+
+
+#include "calc_rmsd_from_one_structure.h"
+#include "en_boltzmann_mixing_stuff.h"
+#include "integrator_ld_Vanden_Eijnden_Cicotti.h"
+#include "md_ld_common_d_dimension_namd.h"
+#include "output.h"
+#include "write_CA_PDB_files.h"
+#include "write_pdb_atom_record.h"
+#include "wrtie_configuration.h"
+
+
+void Perform_langevin_dynamics(FR_DAT *fr, struct simudetails *SimulParam, struct langevin *Langevin_info, rvec *accelerations_old, rvec *accelerations_new, struct integrator_langenvin_VE_C *Integrator_struct, FR_DAT **coordinates_all_structures, int Num_input_structures, double ***array_of_pair_distance_matrices, double **force_constants_all_pairs, double **sigmas_for_repulsive_part, double **epsilons_for_repulsive_part, double *array_of_mixing_parameters, double *aray_of_cutoff_distances, double energy_difference_from_first_structure, double *Average_kinetic_enenrgy);
+
+void Perform_langevin_dynamics_cons(FR_DAT *fr, struct simudetails *SimulParam, struct langevin *Langevin_info, rvec *accelerations_old, rvec *accelerations_new, struct integrator_langenvin_VE_C *Integrator_struct, FR_DAT **coordinates_all_structures, int Num_input_structures, double ***array_of_pair_distance_matrices, double **force_constants_all_pairs, double **sigmas_for_repulsive_part, double **epsilons_for_repulsive_part, double *array_of_mixing_parameters, double *aray_of_cutoff_distances, double energy_difference_from_first_structure, double *Average_kinetic_enenrgy, collective_variables *cons_distances, int Num_cv, double KK);
+
+void Perform_langevin_dynamics_harm(FR_DAT *fr, struct simudetails *SimulParam, struct langevin *Langevin_info, rvec *accelerations_old, rvec *accelerations_new, struct integrator_langenvin_VE_C *Integrator_struct, FR_DAT **coordinates_all_structures, int Num_input_structures, double ***array_of_pair_distance_matrices, double **force_constants_all_pairs, double **sigmas_for_repulsive_part, double **epsilons_for_repulsive_part, double *array_of_mixing_parameters, double *aray_of_cutoff_distances, double energy_difference_from_first_structure, double *Average_kinetic_enenrgy, FR_DAT fix_position, double Kharm);
+
+void Perform_langevin_dynamics_cons_harm(FR_DAT *fr, struct simudetails *SimulParam, struct langevin *Langevin_info, rvec *accelerations_old, rvec *accelerations_new, struct integrator_langenvin_VE_C *Integrator_struct, FR_DAT **coordinates_all_structures, int Num_input_structures, double ***array_of_pair_distance_matrices, double **force_constants_all_pairs, double **sigmas_for_repulsive_part, double **epsilons_for_repulsive_part, double *array_of_mixing_parameters, double *aray_of_cutoff_distances, double energy_difference_from_first_structure, double *Average_kinetic_enenrgy, collective_variables *cons_distances, int Num_cv, FR_DAT fix_position, double KK, double Kharm);
+
+void Perform_langevin_dynamics_harm_omp(FR_DAT *fr, struct simudetails *SimulParam, struct langevin *Langevin_info, rvec *accelerations_old, rvec *accelerations_new, struct integrator_langenvin_VE_C *Integrator_struct, FR_DAT **coordinates_all_structures, int Num_input_structures, double ***array_of_pair_distance_matrices, double **force_constants_all_pairs, double **sigmas_for_repulsive_part, double **epsilons_for_repulsive_part, double *array_of_mixing_parameters, double *aray_of_cutoff_distances, double energy_difference_from_first_structure, double *Average_kinetic_enenrgy, FR_DAT fix_position, double Kharm, int Num_atoms, struct drand48_data *buffer);
+
+void Perform_langevin_dynamics_cons_harm_omp(FR_DAT *fr, struct simudetails *SimulParam, struct langevin *Langevin_info, rvec *accelerations_old, rvec *accelerations_new, struct integrator_langenvin_VE_C *Integrator_struct, FR_DAT **coordinates_all_structures, int Num_input_structures, double ***array_of_pair_distance_matrices, double **force_constants_all_pairs, double **sigmas_for_repulsive_part, double **epsilons_for_repulsive_part, double *array_of_mixing_parameters, double *aray_of_cutoff_distances, double energy_difference_from_first_structure, double *Average_kinetic_enenrgy, collective_variables *cons_distances, int Num_cv, FR_DAT fix_position, double KK, double Kharm, int Num_atoms, struct drand48_data *buffer);
+#endif
Added: SwiftApps/CMTS/stringmethod/src/potential-energies
===================================================================
Added: SwiftApps/CMTS/stringmethod/src/read_configuration.c
===================================================================
--- SwiftApps/CMTS/stringmethod/src/read_configuration.c (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/read_configuration.c 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,254 @@
+/* Reads starting configuration from a file. The input file is a text file. This file only
+ contains coordinate information. Velocities and forces are not stored.*/
+
+
+/* last modified on November 05, 2011*/
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <string.h>
+#include <time.h>
+
+#include "read_configuration.h"
+
+
+/* Format of the input file:
+---------------------------------------------------------------
+Number of atoms
+Box length (one number, cubic box)
+<blank line>
+x_coordinate_of_particle_1 y_coordinate_of_particle_1 z_coordinate_of_particle_1
+x_coordinate_of_particle_2 y_coordinate_of_particle_2 z_coordinate_of_particle_2
+etc. total no. of lines should be equal to total number of atoms
+*/
+/* Reads the config file. It is assumed that required memory has already been allocated.
+ Performs a consistency check to see whether the total numbers of atoms are consistent*/
+void Read_config(FR_DAT *fr, char *input_filename, int Num_particles_from_top)
+{
+ int i, d;
+ int dim = DIMENSION;
+ FILE *in;
+ double box_length_cubic;
+
+ in = fopen(input_filename, "r");
+ if(in == NULL)
+ {
+ printf("File '%s' not found\n", input_filename);
+ exit(1);
+ }
+
+ fscanf(in, "%d ", &fr->natoms);
+ if(Num_particles_from_top != fr->natoms)
+ {
+ printf("Number of particles in input cofiguration file is different from that in topology file\n");
+ exit(1);
+ }
+
+ fscanf(in, "%lf ", &box_length_cubic);
+ for(i = 0 ; i < dim ; i++)
+ {
+ fr->box[i][i] = box_length_cubic;
+ fr->box_dim2[i] = box_length_cubic / 2;
+ }
+
+ /* read particle coordinates*/
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ //fscanf(in, "%lf %lf %lf ", &fr->x[i][0], &fr->x[i][1], &fr->x[i][2]);
+ for(d = 0 ; d < dim ; d++)
+ {
+ fscanf(in, "%lf ", &fr->x[i][d]);
+ }
+ }
+
+ fclose(in);
+
+}
+
+
+
+/* Read the initial configuration and allocate necessary memory
+ * Format of the initial configuration file is same as above.
+ */
+void Read_config_alloc(FR_DAT *fr, char *input_filename)
+{
+ int i, d;
+ int dim = DIMENSION;
+ FILE *in;
+ double box_length_cubic;
+
+ in = fopen(input_filename, "r");
+ if(in == NULL)
+ {
+ printf("File '%s' not found\n", input_filename);
+ exit(1);
+ }
+
+ fscanf(in, "%d ", &fr->natoms);
+
+ /*allocate memory*/
+ fr->x = (rvec *)malloc(fr->natoms * sizeof(rvec));
+ fr->f = (rvec *)malloc(fr->natoms * sizeof(rvec));
+ fr->v = (rvec *)malloc(fr->natoms * sizeof(rvec));
+ fr->m = (double *)malloc(fr->natoms * sizeof(double));
+
+ fscanf(in, "%lf ", &box_length_cubic);
+ for(i = 0 ; i < dim ; i++)
+ {
+ fr->box[i][i] = box_length_cubic;
+ fr->box_dim2[i] = box_length_cubic / 2;
+ }
+
+ /* read particle coordinates*/
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ //fscanf(in, "%lf %lf %lf ", &fr->x[i][0], &fr->x[i][1], &fr->x[i][2]);
+ for(d = 0 ; d < dim ; d++)
+ {
+ fscanf(in, "%lf ", &fr->x[i][d]);
+ }
+ }
+
+ fclose(in);
+
+}
+
+
+/* Read the initial config file in simple format. No box length, the file consists of only
+ * coordinates of all the atoms/sites. The number of atoms read from the file is checked with
+ * the number of atoms input from other source. This is suitable for non-periodic system
+ * where box length is irrelevant. It also allocates the required memory
+ * Format:
+ * Each line should have three numbers separated by white space giving x, y, and z cooridnates of one atom.
+ * */
+void Read_alloc_config_simple_3d(int Num_atoms, FR_DAT *fr, char *input_filename)
+{
+ //int d;
+ //int dim = DIMENSION;
+ FILE *in;
+ char line[1000000];
+ int Num_lines;
+ //double val;
+ double x, y, z;
+
+ in = fopen(input_filename, "r");
+ if(in == NULL)
+ {
+ printf("File '%s' not found\n", input_filename);
+ exit(1);
+ }
+
+ fr->natoms = Num_atoms;
+ fr->x = (rvec *)malloc(fr->natoms * sizeof(rvec));
+ fr->f = (rvec *)malloc(fr->natoms * sizeof(rvec));
+ fr->v = (rvec *)malloc(fr->natoms * sizeof(rvec));
+ fr->m = (double *)malloc(fr->natoms * sizeof(double));
+
+ /*Read coordinates*/
+ Num_lines = 0;
+ while(fgets(line, 1000000, in) != NULL)
+ {
+ if((Num_lines + 1) > Num_atoms)
+ {
+ printf("Number of atoms in file '%s' is more than the expected number of %d. Ignoring stuff after line %d\n", input_filename, Num_atoms, Num_lines);
+ return;
+ }
+ /*for(d = 0 ; d < dim ; d++)
+ {
+ sscanf(line, "%lf", &val);
+ fr->x[Num_lines][d] = val;
+ }*/
+ //sscanf(line, "%lf %lf %lf", &x, &y, &z);
+ //one_coordinate_set->x[Num_lines][0] = x;
+ //one_coordinate_set->x[Num_lines][1] = y;
+ //one_coordinate_set->x[Num_lines][2] = z;
+ sscanf(line, "%lf %lf %lf", &x, &y, &z);
+ fr->x[Num_lines][0] = x;
+ fr->x[Num_lines][1] = y;
+ fr->x[Num_lines][2] = z;
+ Num_lines = Num_lines + 1;
+ }
+ fclose(in);
+ /*Check if number of lines is less than number of atoms*/
+ if(Num_lines < Num_atoms)
+ {
+ printf("Number of lines in file '%s' (%d) is less than the expected number of atoms (%d).\n", input_filename, Num_lines, Num_atoms);
+ exit(1);
+ }
+ else
+ {
+ return;
+ }
+}
+
+
+
+/* Read the initial config file in simple format. No box length, the file consists of only
+ * coordinates of all the atoms/sites. The number of atoms read from the file is checked with
+ * the number of atoms input from other source. This is suitable for non-periodic system
+ * where box length is irrelevant.
+ * DOES NOT ALLOCATE REQUIRED MEMORY.
+ * Format:
+ * Each line should have three numbers separated by white space giving x, y, and z cooridnates of one atom.
+ * THIS IS APPLICABLE FOR THREE DIMENSIONAL SYSTEMS.
+ * */
+void Read_config_simple_3d(int Num_atoms, FR_DAT *fr, char *input_filename)
+{
+ //int d;
+ //int dim = DIMENSION;
+ FILE *in;
+ char line[1000000];
+ int Num_lines;
+ //double val;
+ double x, y, z;
+
+ in = fopen(input_filename, "r");
+ if(in == NULL)
+ {
+ printf("File '%s' not found\n", input_filename);
+ exit(1);
+ }
+
+ /*fr->natoms = Num_atoms;
+ fr->x = (rvec *)malloc(fr->natoms * sizeof(rvec));
+ fr->f = (rvec *)malloc(fr->natoms * sizeof(rvec));
+ fr->v = (rvec *)malloc(fr->natoms * sizeof(rvec));
+ fr->m = (double *)malloc(fr->natoms * sizeof(double));*/
+
+ /*Read coordinates*/
+ Num_lines = 0;
+ while(fgets(line, 1000000, in) != NULL)
+ {
+ if((Num_lines + 1) > Num_atoms)
+ {
+ printf("Number of atoms in file '%s' is more than the expected number of %d. Ignoring stuff after line %d\n", input_filename, Num_atoms, Num_lines);
+ return;
+ }
+ /*for(d = 0 ; d < dim ; d++)
+ {
+ sscanf(line, "%lf", &val);
+ fr->x[Num_lines][d] = val;
+ }*/
+ sscanf(line, "%lf %lf %lf", &x, &y, &z);
+ fr->x[Num_lines][0] = x;
+ fr->x[Num_lines][1] = y;
+ fr->x[Num_lines][2] = z;
+ //one_coordinate_set->x[Num_lines][0] = x;
+ //one_coordinate_set->x[Num_lines][1] = y;
+ //one_coordinate_set->x[Num_lines][2] = z;
+ Num_lines = Num_lines + 1;
+ }
+ fclose(in);
+ /*Check if number of lines is less than number of atoms*/
+ if(Num_lines < Num_atoms)
+ {
+ printf("Number of lines in file '%s' (%d) is less than the expected number of atoms (%d).\n", input_filename, Num_lines, Num_atoms);
+ exit(1);
+ }
+ else
+ {
+ return;
+ }
+}
Added: SwiftApps/CMTS/stringmethod/src/read_configuration.h
===================================================================
--- SwiftApps/CMTS/stringmethod/src/read_configuration.h (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/read_configuration.h 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,14 @@
+#ifndef _read_configuration_h
+#define _read_configuration_h
+
+#include "md_ld_common_d_dimension_namd.h"
+
+void Read_config(FR_DAT *fr, char *input_filename, int Num_particles_from_top);
+
+void Read_config_alloc(FR_DAT *fr, char *input_filename);
+
+void Read_alloc_config_simple_3d(int Num_atoms, FR_DAT *fr, char *input_filename);
+
+void Read_config_simple_3d(int Num_atoms, FR_DAT *fr, char *input_filename);
+
+#endif
Added: SwiftApps/CMTS/stringmethod/src/read_langevin_parameters.c
===================================================================
--- SwiftApps/CMTS/stringmethod/src/read_langevin_parameters.c (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/read_langevin_parameters.c 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,99 @@
+/*
+ Reads friction coefficients for Langevin dynamics.
+ Same friction coefficient for all componenets of a single particle.
+ But different particle can have different friction coefficients.
+*/
+
+/* Last modified on November 01, 2011*/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <string.h>
+#include <time.h>
+
+
+#include "read_langevin_parameters.h"
+
+
+/*reads friction coefficients for Langevin dynamics simulation.
+ * It also populates the array called 'sigma_langevin'.
+ * (See 'md_ld_common_d_dimension.h').
+ The filename is : LANGEVIN_FRICTION
+ Format:
+ NUM_PARTICLES (number of particles %d)
+ Value of friction coefficients. One value per line (in the unit of fs^{-1})
+*/
+void ReadFrictionCoefficients(struct langevin *Langevin_info, double temperature, double Boltzmann_constant, FR_DAT fr)
+{
+ char string[1000];
+ FILE* indata1;
+ int Num_particles_for_check;
+ int i;
+
+ indata1 = fopen("LANGEVIN_FRICTION", "r");
+ if (indata1 == NULL)
+ {
+ printf ("Input file named 'LANGEVIN_FRICTION' not found. Exiting program\n");
+ exit(1);
+ }
+
+ fscanf(indata1, "%s %d", string, &Num_particles_for_check);
+ if(Num_particles_for_check != fr.natoms)
+ {
+ printf("Number of particles read from 'LANGEVIN_FRICTION' is different from other inputs.\n");
+ exit(1);
+ }
+
+ /*allocate memory*/
+ Langevin_info->gamma = (double*)malloc(fr.natoms * sizeof(double));
+ Langevin_info->sigma_langevin = (double*)malloc(fr.natoms * sizeof(double));
+
+ for(i = 0 ; i < fr.natoms ; i++)
+ {
+ fscanf(indata1, "%lf ", &Langevin_info->gamma[i]);
+ /*convert from fs^{-1} to inverse of internal time unit*/
+ Langevin_info->gamma[i] = Langevin_info->gamma[i] * INVERSE_FS_TO_INVERSE_INTERNAL_TIME;
+ Langevin_info->sigma_langevin[i] = sqrt((2.0 * Boltzmann_constant * temperature * Langevin_info->gamma[i]) / fr.m[i]);
+ }
+
+ fclose(indata1);
+}
+
+
+void ReadFrictionCoefficients2(struct langevin *Langevin_info, double temperature, double Boltzmann_constant, FR_DAT fr)
+{
+ char string[1000];
+ FILE* indata1;
+ int Num_particles_for_check;
+ int i;
+
+ indata1 = fopen("LANGEVIN_FRICTION_2", "r");
+ if (indata1 == NULL)
+ {
+ printf ("Input file named 'LANGEVIN_FRICTION' not found. Exiting program\n");
+ exit(1);
+ }
+
+ fscanf(indata1, "%s %d", string, &Num_particles_for_check);
+ if(Num_particles_for_check != fr.natoms)
+ {
+ printf("Number of particles read from 'LANGEVIN_FRICTION' is different from other inputs.\n");
+ exit(1);
+ }
+
+ /*allocate memory*/
+ Langevin_info->gamma = (double*)malloc(fr.natoms * sizeof(double));
+ Langevin_info->sigma_langevin = (double*)malloc(fr.natoms * sizeof(double));
+
+ for(i = 0 ; i < fr.natoms ; i++)
+ {
+ fscanf(indata1, "%lf ", &Langevin_info->gamma[i]);
+ /*convert from fs^{-1} to inverse of internal time unit*/
+ Langevin_info->gamma[i] = Langevin_info->gamma[i] * INVERSE_FS_TO_INVERSE_INTERNAL_TIME;
+ Langevin_info->sigma_langevin[i] = sqrt((2.0 * Boltzmann_constant * temperature * Langevin_info->gamma[i]) / fr.m[i]);
+ }
+
+ fclose(indata1);
+}
+
Added: SwiftApps/CMTS/stringmethod/src/read_langevin_parameters.h
===================================================================
--- SwiftApps/CMTS/stringmethod/src/read_langevin_parameters.h (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/read_langevin_parameters.h 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,22 @@
+
+/* Last modified on December 29, 2011*/
+
+#ifndef _read_langevin_parameters_h
+#define _read_langevin_parameters_h
+
+#include "md_ld_common_d_dimension_namd.h"
+
+
+/*reads friction coefficients for Langevin dynamics simulation.
+ * It also populates the array of type called 'sigma_langevin'.
+ * (See 'md_ld_common_d_dimension.h').
+ The filename is : LANGEVIN_FRICTION
+ Format:
+ NUM_PARTICLES (number of particles %d)
+ Value of friction coefficients. One value per line
+*/
+void ReadFrictionCoefficients(struct langevin *Langevin_info, double temperature, double Boltzmann_constant, FR_DAT fr);
+void ReadFrictionCoefficients2(struct langevin *Langevin_info, double temperature, double Boltzmann_constant, FR_DAT fr);
+
+
+#endif
Added: SwiftApps/CMTS/stringmethod/src/read_masses_all_particles.c
===================================================================
--- SwiftApps/CMTS/stringmethod/src/read_masses_all_particles.c (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/read_masses_all_particles.c 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,79 @@
+/* Last updated on August 29, 2011*/
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <string.h>
+#include <time.h>
+
+/* Read the masses of the particles from the file
+ * 'MASSES_PARTICLES'
+ * Format:
+ * NUM_PARTICLES (number of particles %d)
+ * Masses of particles one per line.
+ * */
+
+#include "read_masses_all_particles.h"
+
+/* Memory allocation must be done before calling this function*/
+void Read_masses_all_particles(FR_DAT *fr)
+{
+ char string[1000];
+ FILE* indata1;
+ int Num_particles_for_check;
+ int i;
+
+ indata1 = fopen("MASSES_PARTICLES", "r");
+ if (indata1 == NULL)
+ {
+ printf ("Input file named 'MASSES_PARTICLES' not found. Exiting program\n");
+ exit(1);
+ }
+
+ fscanf(indata1, "%s %d", string, &Num_particles_for_check);
+ if(Num_particles_for_check != fr->natoms)
+ {
+ printf("Number of particles read from 'MASSES_PARTICLES' is different from other inputs.\n");
+ exit(1);
+ }
+
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ fscanf(indata1, "%lf ", &fr->m[i]);
+ }
+
+ fclose(indata1);
+
+}
+
+void Read_masses_all_particles2(FR_DAT *fr)
+{
+ char string[1000];
+ FILE* indata1;
+ int Num_particles_for_check;
+ int i;
+
+ indata1 = fopen("MASSES_PARTICLES_2", "r");
+ if (indata1 == NULL)
+ {
+ printf ("Input file named 'MASSES_PARTICLES' not found. Exiting program\n");
+ exit(1);
+ }
+
+ fscanf(indata1, "%s %d", string, &Num_particles_for_check);
+ if(Num_particles_for_check != fr->natoms)
+ {
+ printf("Number of particles read from 'MASSES_PARTICLES' is different from other inputs.\n");
+ exit(1);
+ }
+
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ fscanf(indata1, "%lf ", &fr->m[i]);
+ }
+
+ fclose(indata1);
+
+}
+
Added: SwiftApps/CMTS/stringmethod/src/read_masses_all_particles.h
===================================================================
--- SwiftApps/CMTS/stringmethod/src/read_masses_all_particles.h (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/read_masses_all_particles.h 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,10 @@
+#ifndef _read_masses_all_particles_h
+#define _read_masses_all_particles_h
+
+#include "md_ld_common_d_dimension_namd.h"
+
+
+void Read_masses_all_particles(FR_DAT *fr);
+void Read_masses_all_particles2(FR_DAT *fr);
+
+#endif
Added: SwiftApps/CMTS/stringmethod/src/read_simulation_parameters.c
===================================================================
--- SwiftApps/CMTS/stringmethod/src/read_simulation_parameters.c (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/read_simulation_parameters.c 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,91 @@
+/*
+ Reads details of an MD run
+*/
+
+/* Last modified on December 05, 2011*/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <string.h>
+#include <time.h>
+
+
+#include "read_simulation_parameters.h"
+
+
+/*reads parameters for the MD simulation
+ The filename is : 'SIMULPARAMS_NAMD_UNIT'
+ Format:
+ RUN_LENGTH_TIME_STEPS (run length in time steps %d)
+ TIMESTEP (timestep in femto second %lf)
+ COLLISION_FREQUENCY_TIMESTEP (frequency of thermalizing collisions in timestep %d)
+ TEMPERATURE (temperature in kelvin %lf)
+ CONFIG_SAVE_FREQUENCY (frequency of saving configuration to disk in timestep unit %d)
+ PROGRESS_FREQUENCY (frequency for writing the information about the progress of the calculation in timestep %d)
+ WRITE_FREQUENCY_OTHER (frequency for writing other stuff like kinetic energy, potential energy etc. in timestep unit %d)
+ WRITE_FREQUENCY_RMSD (frequency for writing rmsd from initial structure or two end structures in
+ timestep unit. %d)
+ WRITE_FREQUENCY_PDB_TRAJ (frequency for writing configuration to the PDB trajectory file %d. This is
+ mainly for visualization purpose. This is also in the unit of time step)
+*/
+void ReadSimuDetails(struct simudetails *SimulParam, double *temperature)
+{
+ double value;
+ char string[1000];
+ FILE* indata1;
+
+ indata1 = fopen("SIMULPARAMS_NAMD_UNIT", "r");
+ if (indata1 == NULL)
+ {
+ printf ("Input file named 'SIMULPARAMS_NAMD_UNIT' not found. Exiting program\n");
+ exit(1);
+ }
+
+ fscanf(indata1, "%s %lu", string, &(SimulParam->RUNLENGTH));
+ if(SimulParam->RUNLENGTH == 0)
+ {
+ printf("Invalid entry for RUNLENGTH. Exiting program.\n");
+ exit(1);
+ }
+
+ fscanf(indata1,"%s %lf",string, &(SimulParam->timestep));
+ if(SimulParam->timestep <= 0.000000)
+ {
+ printf("Invalid entry for timestep. Exiting program.\n");
+ exit(1);
+ }
+
+ fscanf(indata1,"%s %d", string, &(SimulParam->ColliFreqInTimestep));
+
+ fscanf(indata1,"%s %lf", string, &value);
+ *temperature = value;
+
+ /*
+ fscanf(indata1, "%d", &(SimulParam->NumFrames));
+ if((SimulParam->NumFrames <= 0))
+ {
+ printf("NumFrames should be positive. Please check input\n");
+ exit(1);
+ }
+ fscanf(indata1, "%lf", &(SimulParam->MaxDistForRDF));
+ fscanf(indata1, "%lf", &(SimulParam->deltar));*/
+
+ fscanf(indata1, "%s %lu", string, &(SimulParam->ConfigSaveFreqTimeStep));
+
+ fscanf(indata1, "%s %lu", string, &(SimulParam->ProgressFreqTimeStep));
+
+ fscanf(indata1, "%s %lu", string, &(SimulParam->WriteFreqTimestep));
+
+ fscanf(indata1, "%s %lu", string, &(SimulParam->WriteFreqRMSD));
+
+ fscanf(indata1, "%s %lu", string, &(SimulParam->WriteFreqPDBtraj));
+
+ fclose(indata1);
+
+ /*Ceonvert timestep from femotosecond to internal time unit*/
+ SimulParam->timestep = SimulParam->timestep * FS_TO_INTERNAL_TIME;
+
+}
+
+
Added: SwiftApps/CMTS/stringmethod/src/read_simulation_parameters.h
===================================================================
--- SwiftApps/CMTS/stringmethod/src/read_simulation_parameters.h (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/read_simulation_parameters.h 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,9 @@
+#ifndef _read_simulation_parameters_h
+#define _read_simulation_parameters_h
+
+#include "md_ld_common_d_dimension_namd.h"
+
+
+void ReadSimuDetails(struct simudetails *SimulParam, double *temperature);
+
+#endif
Added: SwiftApps/CMTS/stringmethod/src/read_velocities.c
===================================================================
--- SwiftApps/CMTS/stringmethod/src/read_velocities.c (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/read_velocities.c 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,62 @@
+/* Reads a text file with velocities of the particles.*/
+
+/* last modified on August 30, 2011*/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <string.h>
+#include <time.h>
+
+#include "read_velocities.h"
+
+
+/* Format of the input file:
+---------------------------------------------------------------
+Number of atoms
+<blank line>
+x_velocity_of_particle_1 y_velocity_of_particle_1 z_velocity_of_particle_1
+x_velocity_of_particle_2 y_velocity_of_particle_2 z_velocity_of_particle_2
+etc. total no. of lines should be equal to total number of atoms
+*/
+/* Assumes that memory for velocity array has already been allocated. Returns 1 if file
+ * read is successful otherwise returns 0.*/
+int Read_velocities(FR_DAT *fr, char *input_filename)
+{
+ int i, d;
+ int dim = DIMENSION;
+ FILE *in;
+ int Num_atoms;
+
+ in = fopen(input_filename, "r");
+ if(in == NULL)
+ {
+ return 0;
+ }
+ else
+ {
+ fscanf(in, "%d ", &Num_atoms);
+
+ if(Num_atoms != fr->natoms)
+ {
+ printf("Number of atoms specified in the velocity file is not equal to that in the configuration file\n");
+ exit(1);
+ }
+
+
+ /* read particle velocities*/
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ //fscanf(in, "%lf %lf %lf ", &fr->v[i][0], &fr->v[i][1], &fr->v[i][2]);
+ for(d = 0 ; d < dim ; d++)
+ {
+ fscanf(in, "%lf ", &fr->v[i][d]);
+ }
+ }
+
+ fclose(in);
+ return 1;
+ }
+}
+
+
Added: SwiftApps/CMTS/stringmethod/src/read_velocities.h
===================================================================
--- SwiftApps/CMTS/stringmethod/src/read_velocities.h (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/read_velocities.h 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,8 @@
+#ifndef _read_velocities_h
+#define _read_velocities_h
+
+#include "md_ld_common_d_dimension_namd.h"
+
+int Read_velocities(FR_DAT *fr, char *input_filename);
+
+#endif
Added: SwiftApps/CMTS/stringmethod/src/stringmethod
===================================================================
(Binary files differ)
Property changes on: SwiftApps/CMTS/stringmethod/src/stringmethod
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: SwiftApps/CMTS/stringmethod/src/stringmethod.c
===================================================================
--- SwiftApps/CMTS/stringmethod/src/stringmethod.c (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/stringmethod.c 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,917 @@
+/* Code for Langevin Dynamics simulation for a tw ostate elastic network
+ * model. This is meant for models for protein backbone where only C-alpha
+ * atoms are considered.
+ *
+ * For integration the integrator described in the follwoing paper is
+ * is used:
+ *
+ * Vanden-Eijnden and Ciccotti Chem. Phys. Lett. vol 429, pp 310-316, 2006*/
+
+/* This code does not use periodic boundary condition.*/
+
+/* The main dynamics loop resides in a subroutine whcih is called from the
+ * the main program.*/
+
+/*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~*/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <time.h>
+#include <string.h>
+#include <unistd.h>
+#include <omp.h>
+
+#include "include_all.h"
+#define DIMM 32 //number of images along the string
+#define NSTP1 70000 //steps for constrained dynamics
+#define NSTP2A 5000 //steps for free dynamics
+#define NCYC 100 // number of free dynamics swarms
+#define OUTCYC 1000 //number of iterations of the entire string method
+#define Num_cv 190 /* \ */
+#define Num_cv2 513 // --number of collective variables
+#define Num_cv3 18 // /
+#define TSTP1 0.01 //timestep for free/constrained dynamics
+#define Barrier 0.005 //energy barrier related parameter
+
+void Copy_fr(FR_DAT fr, FR_DAT *copy_of_fr);
+void Save_collective_variables(FR_DAT copy_of_fr, collective_variables *sum_distances);
+void Repar(collective_variables **update_distances);
+void Repar2(collective_variables **update_distances);
+void Init_fr(FR_DAT fr, FR_DAT *copy_of_fr);
+void Clear_positions(FR_DAT *sum_of_fr);
+void Sum_positions(FR_DAT fr, FR_DAT *sum_of_fr);
+void Average_positions(FR_DAT *sum_of_fr);
+void Fix_distances( collective_variables **update_distances, collective_variables **charmm_distances, collective_variables **diff_distances);
+void Add_fix_distances(collective_variables **update_distances, collective_variables **diff_distances);
+void Read_from_fine_grain(FR_DAT *fr, FR_DAT fr2, int coarse_grain_id[]);
+void Save_extra_constraint(FR_DAT copy_of_fr, collective_variables *sample_distances);
+void Save_extra_constraint2(FR_DAT copy_of_fr, collective_variables *sample_distances);
+
+
+int main(int argc, char *argv[])
+{
+
+ int th_id, nthreads;
+
+ struct drand48_data buffer;
+
+ #pragma omp parallel private(th_id)
+ {
+ th_id = omp_get_thread_num();
+ #pragma omp barrier
+ if(th_id==0){
+ nthreads = omp_get_num_threads();
+ if(nthreads < DIMM){
+ printf("WARNING: Number of threads fewer than DIMM\n");
+
+ }
+
+ }
+ }
+
+
+ int coarse_grain_id[]= {0, 2, 4, 6, 8, 10, 11, 13, 15, 17, 19, 21, 23, 25, 26, 28, 30, 32, 34, 36};
+
+ double KK=200.0, KK2=0.0;
+ double Kharm=atof(argv[2]);
+
+ char tempname[1000];
+ char file_ad[100];
+ strcpy(file_ad, argv[1]);
+
+ time_t start, end;
+ time(&start);
+
+ int dim;
+
+ double temperature;
+ double Boltzmann_constant;
+
+ /*Structure for storing position, velocity, force mass etc. main data structure seen by the dynamics routines*/
+ FR_DAT fr[DIMM], copy_of_fr_omp[DIMM], sum_of_fr;
+ //FR_DAT diff_of_fr, diff_of_fr2;
+ FR_DAT fr2[DIMM], copy_of_fr_omp2[DIMM], sum_of_fr2;
+ /*Structure for storing simulation parameters like time-step. length of run etc.*/
+ struct simudetails SimulParam;
+ /*Structure for storing Langevin friction coefficients.*/
+ struct langevin Langevin_info;
+ struct langevin Langevin_info2;
+ /*Structure for implementing the integrator*/
+ struct integrator_langenvin_VE_C Integrator_struct;
+ struct integrator_langenvin_VE_C Integrator_struct2;
+ /* Arrays for storing the accelerations. These are used for integrations*/
+ rvec *accelerations_old[DIMM];
+ rvec *accelerations_new[DIMM];
+ rvec *accelerations_old2[DIMM];
+ rvec *accelerations_new2[DIMM];
+
+ /*Input parameters*/
+ int Num_atoms, Num_atoms2; /*Number of C-alpha atoms*/
+ int Num_input_structures, Num_input_structures2; /*Number of input structures, for two state model Num_input_structures = 2*/
+ double *aray_of_cutoff_distances, *aray_of_cutoff_distances2; /*One value per structure. For each structure the same value is used
+ for all sites.*/
+ double *array_of_mixing_parameters, *array_of_mixing_parameters2; /*\beta_m s for two consecutive structures*/
+ double repulsive_sigma, repulsive_sigma2; /*one value of sigma is used for the repulsive parts of the all pairs*/
+ double repulsive_epsilon, repulsive_epsilon2; /*one value of epsilon is used for the repulsive parts of all pairs*/
+ double fixed_value_of_force_constant, fixed_value_of_force_constant2; /*In Albert Pan's paper this is set to 0.2 kcal/(mol Angstrom^2)*/
+ double energy_parameter_for_force_constant, energy_parameter_for_force_constant2; /*kcal/mol. \epsilon_k in Pan's paper and the value was set to 0.5*/
+ double energy_difference_from_first_structure, energy_difference_from_first_structure2; /*Energy difference of the second structure from the first one in kcal/mol*/
+
+
+ /*Data structures for storing the force filed information*/
+ double ***array_of_pair_distance_matrices, ***array_of_pair_distance_matrices2; /*Array of matrices where pair distances for input strcuturesare stored.
+ For a two state model we will have 2 matrices for two end states.
+ Each matrix is symmetric with meanlingless diagonal elements (that are set to -1)*/
+ double ***array_of_cutoff_matrices, ***array_of_cutoff_matrices2; /*Each member of the array stores the cutoffs for all pairs for that structure
+ Each matrix is symmetric with meanlingless diagonal elements (that are set to -1)*/
+ double **force_constants_all_pairs, **force_constants_all_pairs2; /*This is a matrix that stores the force constants of all pairs.
+ The matrix is symmetric with meanlingless diagonal elements (
+ that are set to -1)*/
+ double **sigmas_for_repulsive_part, **sigmas_for_repulsive_part2; /*Stores the sigmas for repulsive part for all pairs.
+ Matrix is symmetric with meanlingless diagonal elements (that are set to -1)*/
+ double **epsilons_for_repulsive_part, **epsilons_for_repulsive_part2; /*Stores the epsilons for repulsive part for all pairs.
+ Matrix is symmetric with meanlingless diagonal elements (that are set to -1)*/
+
+ FR_DAT *coordinates_all_structures, *coordinates_all_structures2; /*Array for storing the positions of all the input structures.
+ This is also used for storing some force information in the
+ intermediate states of force calcualtion. The reason is that we
+ have to calcualte forces from elastic network of each structure.*/
+
+
+
+ /* File name for the file with input configuration*/
+ char Filename_input_config[1000];
+ /* File name for the file with final configuration at the end of the run*/
+ char Filename_output_config[1000];
+ /* File name for the trajector file.*/
+ char Filename_trajectory[1000];
+ /* File name for input velocities*/
+// char Filename_input_velocities[1000];
+ /* File name for output velocities*/
+ // char Filename_output_velocities[1000];
+
+ /*file pointers for recording various quantities*/
+ FILE *energy, *progress, *KE, *PE, *pressure, *trajectory;
+ long int Num_frames_in_trajectory; /* Number of frames in the output trajectory*/
+ long int Num_data_other_output; /* Number of data points in output files. This is
+ determined by 'WRITE_FREQUENCY_OTHER' input in the SIMULPARAMS file*/
+
+ double Average_kinetic_enenrgy; /*Average kinetic energy of the run. This is use to calcualte the temperature*/
+ double Average_kinetic_enenrgy2; /*Average kinetic energy of the run. This is use to calcualte the temperature*/
+ long int Num_data_rmsd; /*Number of data points in the RMSD file*/
+ long int Num_frames_PDB_trajectory; /*Num_frames in the PDB trajectory file*/
+ char **Residue_names; /*Three letter codes for all the residues. Given in the 'RESIDUE_NAMES'
+ file. This is used for writing the PDB files.*/
+ char **Atom_names;
+ char **Residue_names2;
+ int i;
+ /********************************************************************************************/
+
+ /* Spatial dimension*/
+ dim = DIMENSION;
+ if(dim != 3)
+ {
+ printf("This is meant for three dimensional systems\n");
+ exit(1);
+ }
+
+ /* Read system information, i.e number of C-alpha atoms, number of input structures, mixing coefficients etc.*/
+ Read_en_info(&Num_atoms, &Num_input_structures, &aray_of_cutoff_distances, &array_of_mixing_parameters, &repulsive_sigma, &repulsive_epsilon, &fixed_value_of_force_constant, &energy_parameter_for_force_constant, &energy_difference_from_first_structure);
+ Read_en_info2(&Num_atoms2, &Num_input_structures2, &aray_of_cutoff_distances2, &array_of_mixing_parameters2, &repulsive_sigma2, &repulsive_epsilon2, &fixed_value_of_force_constant2, &energy_parameter_for_force_constant2, &energy_difference_from_first_structure2);
+ if(Num_input_structures != 2)
+ {
+ printf("This is meant for a two state system. Only two input structures are allowed.\n");
+ exit(1);
+ }
+ Print_en_input(Num_atoms, Num_input_structures, aray_of_cutoff_distances, array_of_mixing_parameters, repulsive_sigma, repulsive_epsilon, fixed_value_of_force_constant, energy_parameter_for_force_constant, energy_difference_from_first_structure);
+ Print_en_input2(Num_atoms2, Num_input_structures2, aray_of_cutoff_distances2, array_of_mixing_parameters2, repulsive_sigma2, repulsive_epsilon2, fixed_value_of_force_constant2, energy_parameter_for_force_constant2, energy_difference_from_first_structure2);
+////////////////////////////
+//change energy barrier
+array_of_mixing_parameters2[0]=Barrier;
+
+////////////////////
+
+ /* Allocate memeory*/
+
+for(i=0;i<DIMM;i++){
+ Alloc_main_data_structure(Num_atoms, &fr[i]);
+ accelerations_old[i] = (rvec *)malloc(fr[i].natoms * sizeof(rvec));
+ accelerations_new[i] = (rvec *)malloc(fr[i].natoms * sizeof(rvec));
+}
+
+for(i=0;i<DIMM;i++){
+ Alloc_main_data_structure(Num_atoms2, &fr2[i]);
+ accelerations_old2[i] = (rvec *)malloc(fr2[i].natoms * sizeof(rvec));
+ accelerations_new2[i] = (rvec *)malloc(fr2[i].natoms * sizeof(rvec));
+}
+
+/***********************/
+/* Allocate memory for copy_of_fr, sum_of_fr, diff_of_fr */
+ for(i=0; i<DIMM; i++){
+ Alloc_main_data_structure(Num_atoms, ©_of_fr_omp[i]);
+ }
+ Alloc_main_data_structure(Num_atoms, &sum_of_fr);
+ // Alloc_main_data_structure(Num_atoms, &diff_of_fr);
+
+ for(i=0; i<DIMM; i++){
+ Alloc_main_data_structure(Num_atoms2, ©_of_fr_omp2[i]);
+ }
+ Alloc_main_data_structure(Num_atoms2, &sum_of_fr2);
+// Alloc_main_data_structure(Num_atoms2, &diff_of_fr2);
+/**********************/
+
+
+ Alloc_en(Num_atoms, Num_input_structures, &array_of_pair_distance_matrices, &array_of_cutoff_matrices, &force_constants_all_pairs, &sigmas_for_repulsive_part, &epsilons_for_repulsive_part, &coordinates_all_structures);
+ Alloc_en(Num_atoms2, Num_input_structures2, &array_of_pair_distance_matrices2, &array_of_cutoff_matrices2, &force_constants_all_pairs2, &sigmas_for_repulsive_part2, &epsilons_for_repulsive_part2, &coordinates_all_structures2);
+
+ /* Read all the input structures*/
+ Read_input_structures(Num_input_structures, &coordinates_all_structures);
+ Read_input_structures2(Num_input_structures2, &coordinates_all_structures2);
+
+ /* Calculate all the pair distances for all the structures*/
+ Calc_pair_distances_all_structures(Num_atoms, Num_input_structures, coordinates_all_structures, array_of_pair_distance_matrices);
+ Print_pair_distances_all_structures(Num_atoms, Num_input_structures, array_of_pair_distance_matrices);
+
+ Calc_pair_distances_all_structures(Num_atoms2, Num_input_structures2, coordinates_all_structures2, array_of_pair_distance_matrices2);
+ Print_pair_distances_all_structures2(Num_atoms2, Num_input_structures2, array_of_pair_distance_matrices2);
+
+ /* Set various quantities e.g. the cutoff distances, the sigmas and epsilons*/
+ Set_various_quantities(Num_atoms, Num_input_structures, array_of_cutoff_matrices, sigmas_for_repulsive_part, epsilons_for_repulsive_part, aray_of_cutoff_distances, repulsive_sigma, repulsive_epsilon);
+
+ Set_various_quantities(Num_atoms2, Num_input_structures2, array_of_cutoff_matrices2, sigmas_for_repulsive_part2, epsilons_for_repulsive_part2, aray_of_cutoff_distances2, repulsive_sigma2, repulsive_epsilon2);
+
+ /* Calculate the force constants*/
+ Set_site_dependent_force_constant_2_state(Num_input_structures, Num_atoms, array_of_pair_distance_matrices, energy_parameter_for_force_constant, fixed_value_of_force_constant, force_constants_all_pairs);
+ Print_force_constants(Num_atoms, force_constants_all_pairs);
+
+ Set_site_dependent_force_constant_2_state(Num_input_structures2, Num_atoms2, array_of_pair_distance_matrices2, energy_parameter_for_force_constant2, fixed_value_of_force_constant2, force_constants_all_pairs2);
+ Print_force_constants2(Num_atoms2, force_constants_all_pairs2);
+
+ /* Read simulation parameters*/
+ ReadSimuDetails(&SimulParam, &temperature); //SimulParam.timestep may change!!!
+
+ /*Read the residue names*/
+ Read_residue_names(Num_atoms, &Residue_names);
+ Read_residue_names2(Num_atoms2, &Atom_names, &Residue_names2);
+
+ /* Read input configuration*/
+for(i=0;i<DIMM;i++){
+ sprintf(Filename_input_config, "./%s/INITIAL_CONFIG_C_ALPHA_%d", file_ad, i);
+ Read_config_simple_3d(Num_atoms, &fr[i], Filename_input_config);
+ /* Write a PDB file with the initial configuration*/
+ sprintf(Filename_output_config, "./%s/initial_config_c_alpha_%d.pdb", file_ad, i);
+ Write_CA_PDB_file(&fr[i], Residue_names, Filename_output_config);
+
+ /* Read mass information*/
+ Read_masses_all_particles(&fr[i]);
+ fr[i].t = 0.0;
+}
+
+for(i=0;i<DIMM;i++){
+ sprintf(Filename_input_config, "./%s/INITIAL_CONFIG_C_ALPHA_2_%d", file_ad, i);
+ Read_config_simple_3d(Num_atoms2, &fr2[i], Filename_input_config);
+ /* Write a PDB file with the initial configuration*/
+ sprintf(Filename_output_config, "./%s/initial_config_c_alpha_2_%d.pdb", file_ad, i);
+ Write_CA_PDB_file2(&fr2[i], Residue_names, Filename_output_config);
+
+ /* Read mass information*/
+ Read_masses_all_particles2(&fr2[i]);
+ fr2[i].t = 0.0;
+}
+
+ /*Initialize copy_of_fr and sum_of_fr*/
+ for(i=0; i<DIMM; i++){
+ Init_fr(fr[0], ©_of_fr_omp[i]);
+ }
+ Init_fr(fr[0], &sum_of_fr);
+ // Init_fr(fr[0], &diff_of_fr);
+
+ for(i=0; i<DIMM; i++){
+ Init_fr(fr2[0], ©_of_fr_omp2[i]);
+ }
+ Init_fr(fr2[0], &sum_of_fr2);
+
+ /* Set boltzmann constant.*/
+ Boltzmann_constant = BOLTZMANN_CONSTANT;
+
+ /* Reads langevin friction coefficients*/
+ ReadFrictionCoefficients(&Langevin_info, temperature, Boltzmann_constant, fr[0]);
+ ReadFrictionCoefficients2(&Langevin_info2, temperature, Boltzmann_constant, fr2[0]);
+
+ /* Allocates and initializes data structure used for integration*/
+ Aolloc_initialize_integration_structure(&Integrator_struct, fr[0], SimulParam);
+ Aolloc_initialize_integration_structure(&Integrator_struct2, fr2[0], SimulParam);
+
+
+ /********************************************************************************************/
+
+ /*Start ouput files*/
+ StartFiles(&SimulParam, &energy, &KE, &PE, &pressure);
+ sprintf(tempname, "./%s/track-progress", file_ad);
+ progress = fopen(tempname, "w");
+ fprintf (progress, "Time (fs) Timestep Potential energy Kinetic energy Total energy Pressure\n");
+
+ FILE *pdb_traj;
+ FILE *pdb_traj2;
+ FILE *rmsd_1, *rmsd_2;
+ FILE *rmsd_1b, *rmsd_2b;
+ FILE *cons_file;
+ FILE *out_r, *out_en;
+ collective_variables cons_distances_omp[DIMM][Num_cv], sample_distances_omp[DIMM][Num_cv], **update_distances, **diff_distances;
+ collective_variables cons_distances_omp2[DIMM][Num_cv+Num_cv2], sample_distances_omp2[DIMM][Num_cv+Num_cv2], **update_distances2;
+ collective_variables cons_distances_fine[DIMM][Num_cv3];
+ int j, k, kk, iter;
+ double sum_distances_omp[DIMM][Num_cv];
+ double sum_distances_omp2[DIMM][Num_cv+Num_cv2];
+ FILE *cv_file;
+
+ update_distances = (collective_variables **)malloc(DIMM*sizeof(collective_variables *));
+ update_distances2 = (collective_variables **)malloc(DIMM*sizeof(collective_variables *));
+ diff_distances = (collective_variables **)malloc(DIMM*sizeof(collective_variables *));
+ for(i=0;i<DIMM;i++){
+ update_distances[i] = (collective_variables *)malloc(Num_cv*sizeof(collective_variables));
+ update_distances2[i] = (collective_variables *)malloc((Num_cv+Num_cv2)*sizeof(collective_variables));
+ diff_distances[i] = (collective_variables *)malloc(Num_cv*sizeof(collective_variables));
+ }
+
+ sprintf(tempname, "./%s/CONSTRAINS-EXT-EXT", file_ad);
+ cons_file=fopen(tempname,"r");
+ if(cons_file==NULL){
+ printf("No constrain file!\n");
+ exit(1);
+ }
+
+ for(j=0;j<Num_cv;j++){
+ fscanf(cons_file, "%d %d", &(cons_distances_omp[0][j].atomi), &(cons_distances_omp[0][j].atomj));
+ cons_distances_omp[0][j].atomi--;
+ cons_distances_omp[0][j].atomj--;
+ for(i=0;i<DIMM;i++){
+ sample_distances_omp[i][j].atomi = cons_distances_omp[0][j].atomi;
+ sample_distances_omp[i][j].atomj = cons_distances_omp[0][j].atomj;
+
+ if(i!=0){
+ cons_distances_omp[i][j].atomi = cons_distances_omp[0][j].atomi;
+ cons_distances_omp[i][j].atomj = cons_distances_omp[0][j].atomj;
+ }
+
+ update_distances[i][j].atomi = cons_distances_omp[0][j].atomi;
+ update_distances[i][j].atomj = cons_distances_omp[0][j].atomj;
+ diff_distances[i][j].atomi = cons_distances_omp[0][j].atomi;
+ diff_distances[i][j].atomj = cons_distances_omp[0][j].atomj;
+ }
+ }
+ fclose(cons_file);
+
+ sprintf(tempname, "./%s/CONSTRAINS-EXT-EXT_2", file_ad);
+ cons_file=fopen(tempname,"r");
+ if(cons_file==NULL){
+ printf("No constrain file2!\n");
+ exit(1);
+ }
+
+ for(j=0;j<Num_cv;j++){
+ fscanf(cons_file, "%d %d", &(cons_distances_omp2[0][j].atomi), &(cons_distances_omp2[0][j].atomj));
+ cons_distances_omp2[0][j].atomi--;
+ cons_distances_omp2[0][j].atomj--;
+ for(i=0;i<DIMM;i++){
+ sample_distances_omp2[i][j].atomi = cons_distances_omp2[0][j].atomi;
+ sample_distances_omp2[i][j].atomj = cons_distances_omp2[0][j].atomj;
+
+ if(i!=0){
+ cons_distances_omp2[i][j].atomi = cons_distances_omp2[0][j].atomi;
+ cons_distances_omp2[i][j].atomj = cons_distances_omp2[0][j].atomj;
+ }
+
+ update_distances2[i][j].atomi = cons_distances_omp2[0][j].atomi;
+ update_distances2[i][j].atomj = cons_distances_omp2[0][j].atomj;
+ }
+ }
+ fclose(cons_file);
+
+ sprintf(tempname, "./%s/CONSTRAINS-EXT-EXT_2b", file_ad);
+ cons_file=fopen(tempname,"r");
+ if(cons_file==NULL){
+ printf("No constrain file2!\n");
+ exit(1);
+ }
+
+ for(j=Num_cv;j<Num_cv+Num_cv2;j++){
+ fscanf(cons_file, "%d %d", &(cons_distances_omp2[0][j].atomi), &(cons_distances_omp2[0][j].atomj));
+ cons_distances_omp2[0][j].atomi--;
+ cons_distances_omp2[0][j].atomj--;
+ for(i=0;i<DIMM;i++){
+
+ sample_distances_omp2[i][j].atomi = cons_distances_omp2[0][j].atomi;
+ sample_distances_omp2[i][j].atomj = cons_distances_omp2[0][j].atomj;
+
+ if(i!=0){
+ cons_distances_omp2[i][j].atomi = cons_distances_omp2[0][j].atomi;
+ cons_distances_omp2[i][j].atomj = cons_distances_omp2[0][j].atomj;
+ }
+ update_distances2[i][j].atomi = cons_distances_omp2[0][j].atomi;
+ update_distances2[i][j].atomj = cons_distances_omp2[0][j].atomj;
+
+ }
+ }
+ fclose(cons_file);
+
+ sprintf(tempname, "./%s/CONSTRAINS-FINE", file_ad);
+ cons_file=fopen(tempname,"r");
+ if(cons_file==NULL){
+ printf("No constrain file2!\n");
+ exit(1);
+ }
+
+ for(j=0;j<Num_cv3;j++){
+ fscanf(cons_file, "%d %d", &(cons_distances_fine[0][j].atomi), &(cons_distances_fine[0][j].atomj));
+ cons_distances_fine[0][j].atomi--;
+ cons_distances_fine[0][j].atomj--;
+ for(i=1;i<DIMM;i++){
+ cons_distances_fine[i][j].atomi = cons_distances_fine[0][j].atomi;
+ cons_distances_fine[i][j].atomj = cons_distances_fine[0][j].atomj;
+ }
+ }
+ fclose(cons_file);
+
+ for(i=0;i<DIMM;i++)
+ Save_collective_variables(fr2[i], update_distances2[i]);
+
+ for(i=0;i<DIMM;i++)
+ Save_extra_constraint(fr2[i], update_distances2[i]);
+
+ for(i=0;i<DIMM;i++)
+ Save_extra_constraint2(fr2[i], cons_distances_fine[i]);//record all the bond length
+
+ sprintf(tempname, "./%s/Collective_variables", file_ad);
+ cv_file=fopen(tempname,"w");
+ sprintf(tempname, "./%s/rmsd_from_structure_1_with_time", file_ad);
+ rmsd_1 = fopen(tempname, "w");
+ sprintf(tempname, "./%s/rmsd_from_structure_2_with_time", file_ad);
+ rmsd_2 = fopen(tempname, "w");
+ sprintf(tempname, "./%s/rmsd_from_structure_1b_with_time", file_ad);
+ rmsd_1b = fopen(tempname, "w");
+ sprintf(tempname, "./%s/rmsd_from_structure_2b_with_time", file_ad);
+ rmsd_2b = fopen(tempname, "w");
+ sprintf(tempname, "./%s/repulsive-potential-energy", file_ad);
+ out_r = fopen(tempname, "w");
+ sprintf(tempname, "./%s/elastic-network-potential-energy", file_ad);
+ out_en = fopen(tempname, "w");
+
+ /***********************/
+/******Start Main loop********/
+
+for(iter=0;iter<OUTCYC;iter++){
+
+ //Record collective variables and RMSDs
+ for(i=0;i<DIMM;i++){
+
+ fprintf(rmsd_1, "%d %.8e %.15e\n", i, fr->t * INTERNAL_TIME_TO_FS, Calc_rmsd(&fr2[i], &coordinates_all_structures2[0]));
+ fprintf(rmsd_2, "%d %.8e %.15e\n", i, fr->t * INTERNAL_TIME_TO_FS, Calc_rmsd(&fr2[i], &coordinates_all_structures2[1]));
+
+ Read_from_fine_grain(&fr[i], fr2[i], coarse_grain_id);
+
+ fprintf(rmsd_1b, "%d %.8e %.15e\n", i, fr->t * INTERNAL_TIME_TO_FS, Calc_rmsd(&fr[i], &coordinates_all_structures[0]));
+ fprintf(rmsd_2b, "%d %.8e %.15e\n", i, fr->t * INTERNAL_TIME_TO_FS, Calc_rmsd(&fr[i], &coordinates_all_structures[1]));
+
+ fprintf(cv_file, "%d %d ", iter, i);
+ for(j=0;j<Num_cv;j+=19)
+ fprintf(cv_file, "%lf ", update_distances2[i][j].dis);
+ fprintf(cv_file, "\n");
+
+ }
+ fflush(rmsd_1);
+ fflush(rmsd_2);
+ fflush(rmsd_1b);
+ fflush(rmsd_2b);
+ fflush(cv_file);
+
+ //RUN CONSTRAINT DYNAMICS
+ SimulParam.RUNLENGTH = NSTP1;
+ SimulParam.timestep = TSTP1;
+ #pragma omp parallel for private( j, k, buffer, tempname, pdb_traj2)
+ for(i=0;i<DIMM;i++){
+ sprintf(tempname, "./%s/trajectory_all_%d.pdb", file_ad, i);
+ if(iter==0)
+ pdb_traj2 = fopen(tempname, "w");
+ else
+ pdb_traj2 = fopen(tempname, "a");
+
+ Write_config_to_a_PDB_trajectory_file_2(pdb_traj2, &fr2[i], Atom_names, Residue_names2, iter);
+ fclose(pdb_traj2);
+
+ seed_rand(omp_get_thread_num(), &buffer);
+
+ for(j=0;j<Num_cv+Num_cv2;j++){
+ cons_distances_omp2[i][j].dis=update_distances2[i][j].dis;
+ }
+
+ // get velocities to start the run
+ getvelocities(&fr2[i], temperature);
+ // removes drift. Drift correction is not necessary for a one particle system.
+ velocenter(&fr2[i]);
+
+ Copy_fr(fr2[i], ©_of_fr_omp2[i]);
+
+
+ getforces_cons_harm_omp(&fr2[i], &coordinates_all_structures2, Num_input_structures2, array_of_pair_distance_matrices2, force_constants_all_pairs2, sigmas_for_repulsive_part2, epsilons_for_repulsive_part2, array_of_mixing_parameters2, aray_of_cutoff_distances2, energy_difference_from_first_structure2, cons_distances_omp2[i], Num_cv+Num_cv2, copy_of_fr_omp2[i], KK, Kharm, Num_atoms2);
+
+ // Calcualte kinetic energy
+ get_kinetic_energy(&fr2[i]);
+
+ Average_kinetic_enenrgy2 = 0.0;
+
+ Perform_langevin_dynamics_cons_harm_omp(&fr2[i], &SimulParam, &Langevin_info2, accelerations_old2[i], accelerations_new2[i], &Integrator_struct2, &coordinates_all_structures2, Num_input_structures2, array_of_pair_distance_matrices2, force_constants_all_pairs2, sigmas_for_repulsive_part2, epsilons_for_repulsive_part2, array_of_mixing_parameters2, aray_of_cutoff_distances2, energy_difference_from_first_structure2, &Average_kinetic_enenrgy2, cons_distances_omp2[i], Num_cv+Num_cv2, copy_of_fr_omp2[i], KK, Kharm, Num_atoms2, &buffer);
+ }
+
+ //RELEASE SWARM, RUN FREE DYNAMICS
+ SimulParam.RUNLENGTH = NSTP2A;
+ SimulParam.timestep = TSTP1;
+ #pragma omp parallel for private( j, k, buffer)
+ for(i=0;i<DIMM;i++){
+
+ for(j=0;j<Num_cv+Num_cv2;j++){
+ sample_distances_omp2[i][j].dis=0;
+ sum_distances_omp2[i][j]=0;
+ }
+
+ seed_rand(omp_get_thread_num(), &buffer);
+
+ for(j=0;j<NCYC;j++){
+ // can i declare copy_of_fr to be private instead of defining an copy_fr array???
+ Copy_fr(fr2[i], ©_of_fr_omp2[i]);
+
+ getvelocities(©_of_fr_omp2[i], temperature);
+ // removes drift. Drift correction is not necessary for a one particle system.*
+ velocenter(©_of_fr_omp2[i]);
+
+ // Calculate forces and potential energy*
+ getforces_cons_harm_omp(©_of_fr_omp2[i], &coordinates_all_structures2, Num_input_structures2, array_of_pair_distance_matrices2, force_constants_all_pairs2, sigmas_for_repulsive_part2, epsilons_for_repulsive_part2, array_of_mixing_parameters2, aray_of_cutoff_distances2, energy_difference_from_first_structure2, cons_distances_fine[i], Num_cv3, fr2[i], KK, Kharm, Num_atoms2);
+
+ // Calcualte kinetic energy*
+ get_kinetic_energy(©_of_fr_omp2[i]);
+
+ Average_kinetic_enenrgy2 = 0.0;
+
+ Perform_langevin_dynamics_cons_harm_omp(©_of_fr_omp2[i], &SimulParam, &Langevin_info2, accelerations_old2[i], accelerations_new2[i], &Integrator_struct2, &coordinates_all_structures2, Num_input_structures2, array_of_pair_distance_matrices2, force_constants_all_pairs2, sigmas_for_repulsive_part2, epsilons_for_repulsive_part2, array_of_mixing_parameters2, aray_of_cutoff_distances2, energy_difference_from_first_structure2, &Average_kinetic_enenrgy2, cons_distances_fine[i], Num_cv3, fr2[i], KK, Kharm, Num_atoms2, &buffer);
+
+ Save_collective_variables(copy_of_fr_omp2[i], sample_distances_omp2[i]);
+ Save_extra_constraint(copy_of_fr_omp2[i], sample_distances_omp2[i]);
+
+ for(k=0;k<Num_cv+Num_cv2;k++)
+ sum_distances_omp2[i][k] +=sample_distances_omp2[i][k].dis;
+ }
+
+ for(j=0;j<Num_cv+Num_cv2;j++){
+ update_distances2[i][j].dis=sum_distances_omp2[i][j]/NCYC;
+ }
+ }
+
+ //Record Structural information
+ #pragma omp parallel for private( j, k, buffer, tempname, pdb_traj)
+ for(i=0;i<DIMM;i++){
+ //from all atom to coarse grain
+ Read_from_fine_grain(&fr[i], fr2[i], coarse_grain_id);
+
+ //Swarm in coarse grained potential
+ sprintf(tempname, "./%s/trajectory_%d.pdb", file_ad, i);
+ if(iter==0)
+ pdb_traj = fopen(tempname, "w");
+ else
+ pdb_traj = fopen(tempname, "a");
+ Write_config_to_a_PDB_trajectory_file_1(pdb_traj, &fr[i], Residue_names, iter);
+
+ fclose(pdb_traj);
+
+ }
+
+ //UPDATE COLLECTIVE VARIABLES, CONSTRAINTS FOR NEXT ITERATION***********
+ Repar(update_distances2);
+ Repar2(update_distances2);
+
+}
+//End of Main loop**********
+
+ fclose(out_r);
+ fclose(out_en);
+ fclose(rmsd_1);
+ fclose(rmsd_2);
+ fclose(rmsd_1b);
+ fclose(rmsd_2b);
+ fclose(energy);
+ fclose(KE);
+ fclose(PE);
+ fclose(progress);
+ fclose(cv_file);
+ //Calculate average kinetic eenrgy of the run*
+ Average_kinetic_enenrgy = Average_kinetic_enenrgy / ((double)SimulParam.RUNLENGTH);
+ //Writes the 'summary' file and bunch of other stuff*
+ WriteSummary(&SimulParam, &fr[0], temperature, Average_kinetic_enenrgy);
+
+ // Writes the final configuration *
+for(i=0;i<DIMM;i++){
+ sprintf(Filename_output_config, "./%s/final_config_c_alpha_%d", file_ad, i);
+ Write_config_simple(&fr[i], Filename_output_config);
+ sprintf(Filename_output_config, "./%s/final_config_c_alpha_%d.pdb", file_ad, i);
+ Write_CA_PDB_file(&fr[i], Residue_names, Filename_output_config);
+ }
+
+ /********************************************************************************************/
+
+ time(&end);
+ double diff = difftime(end, start);
+ FILE *t;
+ sprintf(tempname, "./%s/time_elapsed", file_ad);
+ t = fopen(tempname, "w");
+ fprintf(t," %.15e\n", diff);
+ fclose(t);
+
+ printf("Done !!!!\n");
+
+ return 0;
+}
+
+/**************END OF MAIN ROUTINE****************/
+
+
+void Init_fr(FR_DAT fr, FR_DAT *copy_of_fr){
+
+ int i,j;
+
+ copy_of_fr->natoms = fr.natoms;
+
+ for(i=0; i<fr.natoms; i++){
+ copy_of_fr->m[i]=fr.m[i];
+ for(j=0; j<DIMENSION; j++){
+ copy_of_fr->x[i][j]=0;
+ }
+ }
+
+ copy_of_fr->temperature=fr.temperature;
+ copy_of_fr->t=fr.t;
+
+}
+
+
+void Copy_fr(FR_DAT fr, FR_DAT *copy_of_fr){
+
+ int i,j;
+
+ for(i=0; i<fr.natoms; i++){
+ for(j=0; j<DIMENSION; j++){
+ copy_of_fr->x[i][j]=fr.x[i][j];
+ }
+ }
+}
+
+void Clear_positions(FR_DAT *sum_of_fr){
+
+ int i,j;
+
+ for(i=0; i<sum_of_fr->natoms; i++)
+ for(j=0; j<DIMENSION; j++)
+ sum_of_fr->x[i][j]=0;
+
+}
+
+void Sum_positions(FR_DAT fr, FR_DAT *sum_of_fr){
+
+ int i,j;
+
+ for(i=0; i<sum_of_fr->natoms; i++)
+ for(j=0; j<DIMENSION; j++)
+ sum_of_fr->x[i][j] += fr.x[i][j];
+
+}
+
+
+void Average_positions(FR_DAT *sum_of_fr){
+
+ int i,j;
+
+ for(i=0; i<sum_of_fr->natoms; i++)
+ for(j=0; j<DIMENSION; j++)
+ sum_of_fr->x[i][j] /= NCYC;
+
+}
+
+
+void Fix_distances( collective_variables **update_distances, collective_variables **charmm_distances, collective_variables **diff_distances){
+
+ int i, j;
+
+ for(i=0;i<DIMM;i++)
+ for(j=0;j<Num_cv;j++){
+ diff_distances[i][j].dis=charmm_distances[i][j].dis-update_distances[i][j].dis;
+ }
+
+}
+
+
+void Add_fix_distances(collective_variables **update_distances, collective_variables **diff_distances){
+
+ int i, j;
+
+ for(i=0;i<DIMM;i++)
+ for(j=0;j<Num_cv;j++)
+ update_distances[i][j].dis += diff_distances[i][j].dis;
+
+
+}
+
+
+void Save_collective_variables(FR_DAT copy_of_fr, collective_variables *sample_distances){
+
+ int i,j,a,b;
+ double dist, sq_dist;
+
+ for(i=0;i<Num_cv;i++){
+ sq_dist=0;
+ a=sample_distances[i].atomi;
+ b=sample_distances[i].atomj;
+ for(j=0;j<DIMENSION;j++){
+ dist=copy_of_fr.x[a][j]-copy_of_fr.x[b][j];
+ sq_dist += dist*dist;
+ }
+
+ sample_distances[i].dis = sqrt(sq_dist);
+ }
+
+}
+
+void Repar(collective_variables **update_distances){
+
+ double c[DIMM][Num_cv], cr[DIMM][Num_cv], LL[DIMM], s[DIMM];
+ double scd, cd[Num_cv], L, d;
+ int i, j, k;
+
+ for(i=0;i<DIMM;i++)
+ for(j=0;j<Num_cv;j++)
+ c[i][j]=update_distances[i][j].dis;
+
+
+ for(i=0; i<DIMM; i++)
+ LL[i]=0;
+
+ for(i=1; i<DIMM; i++){
+ scd=0;
+ for(k=0; k<Num_cv; k++){
+ cd[k]=c[i][k]-c[i-1][k];
+ scd +=cd[k]*cd[k];
+ }
+
+ LL[i]=LL[i-1]+sqrt(scd);
+
+ }
+
+ L=LL[DIMM-1];
+
+
+ for(k=0; k<DIMM; k++){
+ s[k]=k*L/(DIMM-1);
+ }
+
+ for(k=0; k<Num_cv; k++){
+ cr[0][k]=c[0][k];
+ cr[DIMM-1][k]=c[DIMM-1][k];
+ }
+
+ for(i=1; i<DIMM-1; i++)
+ for(j=1; j<DIMM; j++)
+ if(LL[j]>=s[i]){
+ scd=0;
+ for(k=0; k<Num_cv; k++){
+ cd[k]=c[j][k]-c[j-1][k];
+ scd += cd[k]*cd[k];
+ }
+
+ d=sqrt(scd);
+
+ for(k=0; k<Num_cv; k++)
+ cr[i][k]=(s[i]-LL[j-1])*cd[k]/d + c[j-1][k];
+
+ break;
+
+ }
+
+ for(i=0; i<DIMM; i++){
+ for(k=0;k<Num_cv;k++){
+ update_distances[i][k].dis=cr[i][k];
+ }
+ }
+
+}
+
+
+
+void Repar2(collective_variables **update_distances){
+
+ double c[DIMM][Num_cv2], cr[DIMM][Num_cv2], LL[DIMM], s[DIMM];
+ double scd, cd[Num_cv2], L, d;
+ int i, j, k;
+
+ for(i=0;i<DIMM;i++)
+ for(j=0;j<Num_cv2;j++)
+ c[i][j]=update_distances[i][j+Num_cv].dis;
+
+
+ for(i=0; i<DIMM; i++)
+ LL[i]=0;
+
+ for(i=1; i<DIMM; i++){
+ scd=0;
+ for(k=0; k<Num_cv2; k++){
+ cd[k]=c[i][k]-c[i-1][k];
+ scd +=cd[k]*cd[k];
+ }
+
+ LL[i]=LL[i-1]+sqrt(scd);
+
+ }
+
+ L=LL[DIMM-1];
+
+
+ for(k=0; k<DIMM; k++){
+ s[k]=k*L/(DIMM-1);
+ }
+
+ for(k=0; k<Num_cv2; k++){
+ cr[0][k]=c[0][k];
+ cr[DIMM-1][k]=c[DIMM-1][k];
+ }
+
+ for(i=1; i<DIMM-1; i++)
+ for(j=1; j<DIMM; j++)
+ if(LL[j]>=s[i]){
+ scd=0;
+ for(k=0; k<Num_cv2; k++){
+ cd[k]=c[j][k]-c[j-1][k];
+ scd += cd[k]*cd[k];
+ }
+
+ d=sqrt(scd);
+
+ for(k=0; k<Num_cv2; k++)
+ cr[i][k]=(s[i]-LL[j-1])*cd[k]/d + c[j-1][k];
+
+ break;
+
+ }
+
+ for(i=0; i<DIMM; i++){
+ for(k=0;k<Num_cv2;k++){
+ update_distances[i][k+Num_cv].dis=cr[i][k];
+ }
+ }
+
+}
+
+void Read_from_fine_grain(FR_DAT *fr, FR_DAT fr2, int coarse_grain_id[]){
+ int i,j;
+ for(i=0; i<fr->natoms; i++){
+ for(j=0; j<DIMENSION; j++){
+ fr->x[i][j]=fr2.x[coarse_grain_id[i]][j];
+ }
+ }
+
+}
+
+void Save_extra_constraint(FR_DAT copy_of_fr, collective_variables *sample_distances){
+
+ int i,j,a,b;
+ double dist, sq_dist;
+
+ for(i=Num_cv;i<Num_cv+Num_cv2;i++){
+ sq_dist=0;
+ a=sample_distances[i].atomi;
+ b=sample_distances[i].atomj;
+ for(j=0;j<DIMENSION;j++){
+ dist=copy_of_fr.x[a][j]-copy_of_fr.x[b][j];
+ sq_dist += dist*dist;
+ }
+
+ sample_distances[i].dis = sqrt(sq_dist);
+ }
+
+}
+
+void Save_extra_constraint2(FR_DAT copy_of_fr, collective_variables *sample_distances){
+
+ int i,j,a,b;
+ double dist, sq_dist;
+
+ for(i=0;i<Num_cv3;i++){
+ sq_dist=0;
+ a=sample_distances[i].atomi;
+ b=sample_distances[i].atomj;
+ for(j=0;j<DIMENSION;j++){
+ dist=copy_of_fr.x[a][j]-copy_of_fr.x[b][j];
+ sq_dist += dist*dist;
+ }
+
+ sample_distances[i].dis = sqrt(sq_dist);
+ }
+
+}
+
Added: SwiftApps/CMTS/stringmethod/src/total-energies
===================================================================
Added: SwiftApps/CMTS/stringmethod/src/write_CA_PDB_files.c
===================================================================
--- SwiftApps/CMTS/stringmethod/src/write_CA_PDB_files.c (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/write_CA_PDB_files.c 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,207 @@
+/* Codes for writing PDB files for C-alpha CG model of a protein.*/
+
+/*Last modified on December 05, 2011*/
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <string.h>
+
+#include "md_ld_common_d_dimension_namd.h"
+#include "write_pdb_atom_record.h"
+
+
+/* Write one configuration of the system to a PDB file. The array of residue
+ * names is supplied as an argument.*/
+void Write_one_CA_config_in_PDB_format(FILE *out, FR_DAT *fr, char **Residue_names)
+{
+ int i, residue_sequence_number;
+ float x, y, z;
+
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ /*need to typecast positions values from double to float*/
+ x = (float)fr->x[i][0];
+ y = (float)fr->x[i][1];
+ z = (float)fr->x[i][2];
+ residue_sequence_number = i + 1;
+ /*write to the file*/
+ Write_one_PDB_ATOM_CA(out, Residue_names[i], residue_sequence_number, x, y, z);
+ }
+
+}
+
+void Write_one_CA_config_in_PDB_format2(FILE *out, FR_DAT *fr, char **Residue_names)
+{
+ int i, residue_sequence_number;
+ float x, y, z;
+ int ca_num[]= {0, 2, 4, 6, 8, 10, 11, 13, 15, 17, 19, 21, 23, 25, 26, 28, 30, 32, 34, 36};
+
+ for(i = 0 ; i < 20 ; i++)
+ {
+ /*need to typecast positions values from double to float*/
+ x = (float)fr->x[ca_num[i]][0];
+ y = (float)fr->x[ca_num[i]][1];
+ z = (float)fr->x[ca_num[i]][2];
+ residue_sequence_number = i + 1;
+ /*write to the file*/
+ Write_one_PDB_ATOM_CA(out, Residue_names[i], residue_sequence_number, x, y, z);
+ }
+
+}
+
+void Write_one_CA_config_in_PDB_format3(FILE *out, FR_DAT *fr, char **Atom_names, char **Residue_names)
+{
+ int i, residue_sequence_number;
+ float x, y, z;
+
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ /*need to typecast positions values from double to float*/
+ x = (float)fr->x[i][0];
+ y = (float)fr->x[i][1];
+ z = (float)fr->x[i][2];
+ residue_sequence_number = i + 1;
+ /*write to the file*/
+ Write_one_PDB_ATOM_CA2(out, Atom_names[i], Residue_names[i], residue_sequence_number, x, y, z);
+ }
+
+}
+
+/* Read residue names from the file 'RESIDUE_NAMES'. Number of lines should be equal to the number of C-alpha atoms.
+ * This code also allocates the necessary memory.*/
+void Read_residue_names(int Num_CA_atoms, char ***Residue_names)
+{
+ int i;
+ FILE *in;
+ char line[1000000], name[4];
+ int Num_lines;
+
+ *Residue_names = (char**)malloc(Num_CA_atoms * sizeof(char*));
+ for(i = 0 ; i < Num_CA_atoms ; i++)
+ {
+ (*Residue_names)[i] = (char*)malloc(4 * sizeof(char));
+ }
+
+ in = fopen("RESIDUE_NAMES", "r");
+ if(in == NULL)
+ {
+ printf("File 'RESIDUE_NAMES' not found\n");
+ exit(1);
+ }
+ Num_lines = 0;
+ while(fgets(line, 1000000, in) != NULL)
+ {
+ if((Num_lines + 1) > Num_CA_atoms)
+ {
+ printf("Number of lines in file 'RESIDUE_NAMES' is more than the number of CA atoms (%d). Something is wrong! \n", Num_CA_atoms);
+ }
+
+ sscanf(line, "%s", name);
+ strcpy((*Residue_names)[Num_lines], name);
+ Num_lines = Num_lines + 1;
+ }
+ fclose(in);
+ /*Check if number of lines is less than number of atoms*/
+ if(Num_lines < Num_CA_atoms)
+ {
+ printf("Number of lines in file 'RESIDUE_NAMES' (%d) is less the number of atoms (%d).\n", Num_lines, Num_CA_atoms);
+ exit(1);
+ }
+}
+
+void Read_residue_names2(int Num_CA_atoms, char *** Atom_names, char ***Residue_names)
+{
+ int i;
+ FILE *in;
+ char line[1000000], name[4], name2[3];
+ int Num_lines;
+
+ *Residue_names = (char**)malloc(Num_CA_atoms * sizeof(char*));
+ *Atom_names = (char**)malloc(Num_CA_atoms * sizeof(char*));
+ for(i = 0 ; i < Num_CA_atoms ; i++)
+ {
+ (*Residue_names)[i] = (char*)malloc(4 * sizeof(char));
+ (*Atom_names)[i] = (char*)malloc(3 * sizeof(char));
+ }
+
+ in = fopen("RESIDUE_NAMES_2", "r");
+ if(in == NULL)
+ {
+ printf("File 'RESIDUE_NAMES' not found\n");
+ exit(1);
+ }
+ Num_lines = 0;
+ while(fgets(line, 1000000, in) != NULL)
+ {
+ if((Num_lines + 1) > Num_CA_atoms)
+ {
+ printf("Number of lines in file 'RESIDUE_NAMES' is more than the number of CA atoms (%d). Something is wrong! \n", Num_CA_atoms);
+ }
+
+ sscanf(line, "%s %s", name2, name);
+ strcpy((*Residue_names)[Num_lines], name);
+ strcpy((*Atom_names)[Num_lines], name2);
+ Num_lines = Num_lines + 1;
+ }
+ fclose(in);
+ /*Check if number of lines is less than number of atoms*/
+ if(Num_lines < Num_CA_atoms)
+ {
+ printf("Number of lines in file 'RESIDUE_NAMES' (%d) is less the number of atoms (%d).\n", Num_lines, Num_CA_atoms);
+ exit(1);
+ }
+}
+
+
+/* Write a PDB file with one configuration of the system. This is a wrapper function*/
+void Write_CA_PDB_file(FR_DAT *fr, char **Residue_names, char File_name_CA_PDB[1000])
+{
+ FILE *out;
+ out = fopen(File_name_CA_PDB, "w");
+ Write_one_CA_config_in_PDB_format(out, fr, Residue_names);
+ fclose(out);
+}
+
+void Write_CA_PDB_file2(FR_DAT *fr, char **Residue_names, char File_name_CA_PDB[1000])
+{
+ FILE *out;
+ out = fopen(File_name_CA_PDB, "w");
+ Write_one_CA_config_in_PDB_format2(out, fr, Residue_names);
+ fclose(out);
+}
+
+/* This function writes a configuration to a PDB trajectory file.
+ * 'config_index' gives the index of the configuration written. It starts from 1 and takes values upto total Number of
+ * trajectories in the file.
+ *
+ * The format of the file. Each config is written in the following way.
+ * MODEL config_index
+ * Info about config in PDB format
+ * ENDMDL
+ *
+ * */
+void Write_config_to_a_PDB_trajectory_file(FILE *out, FR_DAT *fr, char **Residue_names, int config_index)
+{
+ fprintf(out, "MODEL %d\n", config_index);
+ Write_one_CA_config_in_PDB_format(out, fr, Residue_names);
+ fprintf(out, "ENDMDL\n");
+}
+
+
+
+/* Same stuff as above only 'config_index' is long int*/
+void Write_config_to_a_PDB_trajectory_file_1(FILE *out, FR_DAT *fr, char **Residue_names, long int config_index)
+{
+ fprintf(out, "MODEL %lu\n", config_index);
+ Write_one_CA_config_in_PDB_format(out, fr, Residue_names);
+ fprintf(out, "ENDMDL\n");
+}
+
+void Write_config_to_a_PDB_trajectory_file_2(FILE *out, FR_DAT *fr, char **Atom_names, char **Residue_names, long int config_index)
+{
+ fprintf(out, "MODEL %lu\n", config_index);
+ Write_one_CA_config_in_PDB_format3(out, fr, Atom_names, Residue_names);
+ fprintf(out, "ENDMDL\n");
+}
Added: SwiftApps/CMTS/stringmethod/src/write_CA_PDB_files.h
===================================================================
--- SwiftApps/CMTS/stringmethod/src/write_CA_PDB_files.h (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/write_CA_PDB_files.h 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,24 @@
+#ifndef _write_CA_PDB_files_h
+#define _write_CA_PDB_files_h
+
+#include "md_ld_common_d_dimension_namd.h"
+#include "write_pdb_atom_record.h"
+
+
+void Write_one_CA_config_in_PDB_format(FILE *out, FR_DAT *fr, char **Residue_names);
+void Write_one_CA_config_in_PDB_format2(FILE *out, FR_DAT *fr, char **Residue_names);
+void Write_one_CA_config_in_PDB_format3(FILE *out, FR_DAT *fr, char **Atom_names, char **Residue_names);
+
+void Read_residue_names(int Num_CA_atoms, char ***Residue_names);
+
+void Write_CA_PDB_file(FR_DAT *fr, char **Residue_names, char File_name_CA_PDB[1000]);
+void Write_CA_PDB_file2(FR_DAT *fr, char **Residue_names, char File_name_CA_PDB[1000]);
+
+void Write_config_to_a_PDB_trajectory_file(FILE *out, FR_DAT *fr, char **Residue_names, int config_index);
+
+void Write_config_to_a_PDB_trajectory_file_1(FILE *out, FR_DAT *fr, char **Residue_names, long int config_index);
+
+void Read_residue_names2(int Num_CA_atoms, char *** Atom_names, char ***Residue_names);
+
+void Write_config_to_a_PDB_trajectory_file_2(FILE *out, FR_DAT *fr, char **Atom_names, char **Residue_names, long int config_index);
+#endif
Added: SwiftApps/CMTS/stringmethod/src/write_pdb_atom_record.c
===================================================================
--- SwiftApps/CMTS/stringmethod/src/write_pdb_atom_record.c (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/write_pdb_atom_record.c 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,97 @@
+/*Read and write one PDB style ATOM record */
+
+/*Last modified on December 01, 2011*/
+
+
+/* FORTRAN format for writing PDB records
+ * ATOM
+ * HETATM Format(A6,I5,1X,A4,A1,A3,1X,A1,I4,A1,3X,3F8.3,2F6.2,10X,A2,A2)
+ *
+ * HELIX Format(A6,1X,I3,1X,A3,2(1X,A3,1X,A1,1X,I4,A1),I2,A30,1X,I5)
+ *
+ * SHEET Format(A6,1X,I3,1X,A3,I2,2(1X,A3,1X,A1,I4,A1),I2,2(1X,A4,A3,1X,A1,I4,A1))
+ *
+ * SSBOND Format(A6,1X,I3,1X,A3,1X,A1,1X,I4,A1,3X,A3,1X,A1,1X,I4,A1,23X,2(2I3,1X),F5.2)
+ * */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <string.h>
+
+#include "write_pdb_atom_record.h"
+
+
+/* Write one ATOM record for a CA atom to a file. This is suitable for writing output of our
+ * programs that work with C-alpha s only. Relevant fields are supplied as arguments other
+ * fields are populated with generic values.*/
+void Write_one_PDB_ATOM_CA(FILE *out, char residue_name[4], int residue_sequence_number, float x, float y, float z)
+{
+ PDB_ATOM one_PDB_ATOM;
+
+ one_PDB_ATOM.atom_serial_number = residue_sequence_number; /*here atom and residue sare same*/
+ sprintf(one_PDB_ATOM.atom_name, "CA");
+ one_PDB_ATOM.atom_alt_loc = ' ';
+ sprintf(one_PDB_ATOM.residue_name, residue_name);
+ one_PDB_ATOM.chain_id = 'A';
+ one_PDB_ATOM.residue_sequence_number = residue_sequence_number;
+ one_PDB_ATOM.insert_code = ' ';
+ one_PDB_ATOM.x = x;
+ one_PDB_ATOM.y = y;
+ one_PDB_ATOM.z = z;
+ one_PDB_ATOM.occupancy = 1.00;
+ one_PDB_ATOM.temperature_factor = 1.00;
+ sprintf(one_PDB_ATOM.element_symbol, "A");
+ sprintf(one_PDB_ATOM.charge_on_atom, "C");
+
+ Write_one_PDB_ATOM(out, &one_PDB_ATOM);
+}
+
+void Write_one_PDB_ATOM_CA2(FILE *out, char atom_name[3], char residue_name[4], int residue_sequence_number, float x, float y, float z)
+{
+ PDB_ATOM one_PDB_ATOM;
+
+ one_PDB_ATOM.atom_serial_number = residue_sequence_number; /*here atom and residue sare same*/
+ sprintf(one_PDB_ATOM.atom_name, atom_name);
+ one_PDB_ATOM.atom_alt_loc = ' ';
+ sprintf(one_PDB_ATOM.residue_name, residue_name);
+ one_PDB_ATOM.chain_id = 'A';
+ one_PDB_ATOM.residue_sequence_number = residue_sequence_number;
+ one_PDB_ATOM.insert_code = ' ';
+ one_PDB_ATOM.x = x;
+ one_PDB_ATOM.y = y;
+ one_PDB_ATOM.z = z;
+ one_PDB_ATOM.occupancy = 1.00;
+ one_PDB_ATOM.temperature_factor = 1.00;
+ sprintf(one_PDB_ATOM.element_symbol, "A");
+ sprintf(one_PDB_ATOM.charge_on_atom, "C");
+
+ Write_one_PDB_ATOM(out, &one_PDB_ATOM);
+}
+
+/* THIS HAS ALL THE FIELDS. Write one ATOM record to a file.
+ * FORTRAM Format(A6,I5,1X,A4,A1,A3,1X,A1,I4,A1,3X,3F8.3,2F6.2,10X,A2,A2)
+ * The code follows this FORTRAN format which is consistent with the official format.
+ * */
+void Write_one_PDB_ATOM(FILE *out, PDB_ATOM *one_PDB_ATOM)
+{
+ fprintf(out, "ATOM %5d %-4s%c%-3s %c%4d%c %8.3f%8.3f%8.3f%6.2f%6.2f %-2s%-2s\n",
+ one_PDB_ATOM->atom_serial_number,
+ one_PDB_ATOM->atom_name,
+ one_PDB_ATOM->atom_alt_loc,
+ one_PDB_ATOM->residue_name,
+ one_PDB_ATOM->chain_id,
+ one_PDB_ATOM->residue_sequence_number,
+ one_PDB_ATOM->insert_code,
+ one_PDB_ATOM->x,
+ one_PDB_ATOM->y,
+ one_PDB_ATOM->z,
+ one_PDB_ATOM->occupancy,
+ one_PDB_ATOM->temperature_factor,
+ one_PDB_ATOM->element_symbol,
+ one_PDB_ATOM->charge_on_atom);
+}
+
+
+
+
Added: SwiftApps/CMTS/stringmethod/src/write_pdb_atom_record.h
===================================================================
--- SwiftApps/CMTS/stringmethod/src/write_pdb_atom_record.h (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/write_pdb_atom_record.h 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,34 @@
+#ifndef _write_pdb_atom_record_h
+#define _write_pdb_atom_record_h
+
+/* The last two records are compatible with official PBD documentation.
+ * But it appreas that these records can also include charecter id for
+ * segments, i.e. A for protein B for water etc.
+ * Character arrays are C style strings. We have to make space for the extra NULL character
+ * at the end. So the lenghts of fields are one less than the lengths of the character arrays.*/
+typedef struct {
+ int atom_serial_number;
+ char atom_name[5];
+ char atom_alt_loc;
+ char residue_name[4];
+ char chain_id;
+ int residue_sequence_number;
+ char insert_code;
+ float x;
+ float y;
+ float z;
+ float occupancy;
+ float temperature_factor;
+ char element_symbol[3];
+ char charge_on_atom[3];
+}PDB_ATOM;
+
+void Write_one_PDB_ATOM_CA(FILE *out, char residue_name[4], int residue_sequence_number, float x, float y, float z);
+void Write_one_PDB_ATOM_CA2(FILE *out, char atom_name[3], char residue_name[4], int residue_sequence_number, float x, float y, float z);
+
+/* Write one ATOM record to a file.*/
+void Write_one_PDB_ATOM(FILE *out, PDB_ATOM *one_PDB_ATOM);
+
+
+
+#endif
Added: SwiftApps/CMTS/stringmethod/src/write_velocities.c
===================================================================
--- SwiftApps/CMTS/stringmethod/src/write_velocities.c (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/write_velocities.c 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,61 @@
+/* Reads a text file with velocities of the particles.*/
+
+/* last modified on September 06, 2011*/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <string.h>
+#include <time.h>
+
+#include "write_velocities.h"
+
+
+/* Format of the input file:
+---------------------------------------------------------------
+Number of atoms
+<blank line>
+x_velocity_of_particle_1 y_velocity_of_particle_1 z_velocity_of_particle_1
+x_velocity_of_particle_2 y_velocity_of_particle_2 z_velocity_of_particle_2
+etc. total no. of lines should be equal to total number of atoms
+*/
+
+void Write_velocities(FR_DAT *fr, char *output_filename)
+{
+ int i, d;
+ int dim = DIMENSION;
+ FILE *out;
+
+ out = fopen(output_filename, "w");
+
+ fprintf(out, "%d\n\n", fr->natoms);
+
+ /* write particle velocities*/
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ //fprintf(out, "%.15e %.15e %.15e\n", fr->v[i][0], fr->v[i][1], fr->v[i][2]);
+ for(d = 0 ; d < dim ; d++)
+ {
+ fprintf(out, "%.15e ", fr->v[i][d]);
+ }
+ fprintf(out, "\n");
+ }
+
+ fclose(out);
+
+}
+
+
+
+/*Writes x and y components of the velocity to two different files at regular interval*/
+void Write_velocity_to_files(FR_DAT *fr, FILE *output_file_pointer_x, FILE *output_file_pointer_y)
+{
+
+ fprintf(output_file_pointer_x, "%.15e\n", fr->v[0][0]);
+ fprintf(output_file_pointer_y, "%.15e\n", fr->v[0][1]);
+
+}
+
+
+
+
Added: SwiftApps/CMTS/stringmethod/src/write_velocities.h
===================================================================
--- SwiftApps/CMTS/stringmethod/src/write_velocities.h (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/write_velocities.h 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,10 @@
+#ifndef _write_velocities_h
+#define _write_velocities_h
+
+#include "md_ld_common_d_dimension_namd.h"
+
+void Write_velocities(FR_DAT *fr, char *output_filename);
+
+void Write_velocity_to_files(FR_DAT *fr, FILE *output_file_pointer_x, FILE *output_file_pointer_y);
+
+#endif
Added: SwiftApps/CMTS/stringmethod/src/wrtie_configuration.c
===================================================================
--- SwiftApps/CMTS/stringmethod/src/wrtie_configuration.c (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/wrtie_configuration.c 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,174 @@
+/* Writes a configuration file. Used for writing the final configuration at the end of the
+ run. */
+
+/* Last modified on November 01, 2011*/
+
+
+/* Format of the output file:
+---------------------------------------------------------------
+Number of atoms
+Box length (one number, cubic box)
+<blank line>
+x_coordinate_of_particle_1 y_coordinate_of_particle_1 z_coordinate_of_particle_1
+x_coordinate_of_particle_2 y_coordinate_of_particle_2 z_coordinate_of_particle_2
+etc. total no. of lines should be equal to total number of atoms
+*/
+/* Writes a config file. Only coordinates no velocities or forces*/
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <string.h>
+#include <time.h>
+
+#include "wrtie_configuration.h"
+
+void Write_config(FR_DAT *fr, char *output_filename)
+{
+ int i, d;
+ int dim = DIMENSION;
+ FILE *out;
+ double box_length_cubic;
+
+ box_length_cubic = fr->box[0][0];
+
+ out = fopen(output_filename, "w");
+
+ fprintf(out, "%d\n%.15e\n\n", fr->natoms, box_length_cubic);
+
+ /* write particle coordinates*/
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ //fprintf(out, "%.15e %.15e %.15e\n", fr->x[i][0], fr->x[i][1], fr->x[i][2]);
+ for(d = 0 ; d < dim ; d ++)
+ {
+ fprintf(out, "%.15e ", fr->x[i][d]);
+ }
+ fprintf(out, "\n");
+ }
+
+ fclose(out);
+
+}
+
+
+
+/* Writes configurtions (frames) in the trajectory file. This file is used for post
+ processing.
+
+ The format of the file:
+ ----------------------------------------------------------------------------------------
+ No. of atoms
+ No. of frames
+ Box length
+ <Blank line>
+ Coordinates of forces for all the particles. One line for each particle with the follwoing format:
+ coordinate_x coordinate_y coordinate_z force_x force_y force_z
+ ... ... ...
+ <Blank line>
+ same for the next frame
+ ----------------------------------------------------------------------------------------
+
+ This functions writes the infromation for one frame. Data at the begining of the file
+ is writen when the file is first created.
+*/
+
+void Write_config_to_trajectory_file(FR_DAT *fr, FILE *output_file_pointer)
+{
+ int i, d;
+ int dim = DIMENSION;
+
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ //fprintf(output_file_pointer, "%.15e %.15e %.15e %.15e %.15e %.15e\n", fr->x[i][0], fr->x[i][1], fr->x[i][2], fr->f[i][0], fr->f[i][1], fr->f[i][2]);
+ for(d = 0 ; d < dim ; d ++)
+ {
+ fprintf(output_file_pointer, "%.15e ", fr->x[i][d]);
+ }
+ fprintf(output_file_pointer," ");
+ for(d = 0 ; d < dim ; d ++)
+ {
+ fprintf(output_file_pointer, "%.15e ", fr->f[i][d]);
+ }
+ fprintf(output_file_pointer, "\n");
+ }
+ fprintf(output_file_pointer, "\n");
+}
+
+
+
+/* New format for trajectory file. forces are not stored, only coordiates and nothing else.
+ * This will help us to process the trajectory of a one particle model system*/
+void Write_config_to_trajectory_file_only_coordinates(FR_DAT *fr, FILE *output_file_pointer)
+{
+ int i, d;
+ int dim = DIMENSION;
+
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ //fprintf(output_file_pointer, "%.15e %.15e %.15e %.15e %.15e %.15e\n", fr->x[i][0], fr->x[i][1], fr->x[i][2], fr->f[i][0], fr->f[i][1], fr->f[i][2]);
+ for(d = 0 ; d < dim ; d ++)
+ {
+ fprintf(output_file_pointer, "%.15e ", fr->x[i][d]);
+ }
+ //fprintf(output_file_pointer," ");
+ /*for(d = 0 ; d < dim ; d ++)
+ {
+ fprintf(output_file_pointer, "%.15e ", fr->f[i][d]);
+ }
+ */
+ fprintf(output_file_pointer, "\n");
+ }
+ //fprintf(output_file_pointer, "\n");
+}
+
+/* Write config file with only coordinates.
+ * Format:
+ * Each line has the coordinates of an atom separated by white space, starting from x, y, ..etc.*/
+void Write_config_simple(FR_DAT *fr, char *output_filename)
+{
+ int i, d;
+ int dim = DIMENSION;
+ FILE *out;
+
+ out = fopen(output_filename, "w");
+
+ /* write particle coordinates*/
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ for(d = 0 ; d < dim ; d++)
+ {
+ fprintf(out, "%.15e ", fr->x[i][d]);
+ }
+ fprintf(out, "\n");
+ }
+
+ fclose(out);
+
+}
+
+
+/* Wrties a VMD style xyz file. This is needed for visualization.
+ * Format:
+ * First line: number of atom
+ * Second line: a comment
+ * Then for each line
+ * atom name (C) x, y, z
+ * */
+void Write_config_vmd_xyz(FR_DAT *fr, char *output_filename)
+{
+ int i;
+ FILE *out;
+
+ out = fopen(output_filename, "w");
+ fprintf(out, "%d\n", fr->natoms);
+ fprintf(out, " file generated by my program\n");
+ /* write particle coordinates*/
+ for(i = 0 ; i < fr->natoms ; i++)
+ {
+ fprintf(out, " C %lf %lf %lf\n", fr->x[i][0], fr->x[i][1], fr->x[i][2]);
+ }
+
+ fclose(out);
+}
Added: SwiftApps/CMTS/stringmethod/src/wrtie_configuration.h
===================================================================
--- SwiftApps/CMTS/stringmethod/src/wrtie_configuration.h (rev 0)
+++ SwiftApps/CMTS/stringmethod/src/wrtie_configuration.h 2012-10-22 14:57:20 UTC (rev 5984)
@@ -0,0 +1,16 @@
+#ifndef _wrtie_configuration_h
+#define _wrtie_configuration_h
+
+#include "md_ld_common_d_dimension_namd.h"
+
+void Write_config(FR_DAT *fr, char *output_filename);
+
+void Write_config_to_trajectory_file(FR_DAT *fr, FILE *output_file_pointer);
+
+void Write_config_to_trajectory_file_only_coordinates(FR_DAT *fr, FILE *output_file_pointer);
+
+void Write_config_simple(FR_DAT *fr, char *output_filename);
+
+void Write_config_vmd_xyz(FR_DAT *fr, char *output_filename);
+
+#endif
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