[Swift-commit] r5907 - in SwiftApps/CMTS/dimers: . bin conf input_files
davidk at ci.uchicago.edu
davidk at ci.uchicago.edu
Mon Aug 27 02:14:43 CDT 2012
Author: davidk
Date: 2012-08-27 02:14:42 -0500 (Mon, 27 Aug 2012)
New Revision: 5907
Added:
SwiftApps/CMTS/dimers/bin/dimers.sh
SwiftApps/CMTS/dimers/input_files/lammps_new_spherical.in
Removed:
SwiftApps/CMTS/dimers/input_files/end_20.restart.swift
SwiftApps/CMTS/dimers/input_files/end_25.restart.swift
SwiftApps/CMTS/dimers/input_files/end_30.restart.swift
SwiftApps/CMTS/dimers/input_files/end_35.restart.swift
SwiftApps/CMTS/dimers/input_files/end_40.restart.swift
SwiftApps/CMTS/dimers/input_files/end_45.restart.swift
SwiftApps/CMTS/dimers/input_files/end_50.restart.swift
SwiftApps/CMTS/dimers/input_files/end_55.restart.swift
SwiftApps/CMTS/dimers/input_files/end_60.restart.swift
SwiftApps/CMTS/dimers/input_files/end_65.restart.swift
SwiftApps/CMTS/dimers/input_files/end_70.restart.swift
Modified:
SwiftApps/CMTS/dimers/README
SwiftApps/CMTS/dimers/conf/grotthuss.cf
SwiftApps/CMTS/dimers/conf/makena.cf
SwiftApps/CMTS/dimers/dimers.swift
Log:
Use real lammps
Use wrapper script to simplify the example
Modified: SwiftApps/CMTS/dimers/README
===================================================================
--- SwiftApps/CMTS/dimers/README 2012-08-23 18:51:16 UTC (rev 5906)
+++ SwiftApps/CMTS/dimers/README 2012-08-27 07:14:42 UTC (rev 5907)
@@ -10,7 +10,7 @@
Add the following line to $HOME/.bashrc to set the PATH:
-----
-export PATH=/scratch/davidk/swift-trunk/cog/modules/swift/dist/swift-svn/bin:/opt/torque/bin:$PATH
+export PATH=/scratch/davidk/swift-trunk/cog/modules/swift/dist/swift-svn/bin:/scratch/davidk/lammps-12Oct11_spherical_modified/src:/opt/torque/bin:$PATH
-----
You will need to create a directory called /scratch/<yourusername>:
Added: SwiftApps/CMTS/dimers/bin/dimers.sh
===================================================================
--- SwiftApps/CMTS/dimers/bin/dimers.sh (rev 0)
+++ SwiftApps/CMTS/dimers/bin/dimers.sh 2012-08-27 07:14:42 UTC (rev 5907)
@@ -0,0 +1,14 @@
+#!/bin/bash
+
+prev_ndimers_file=$1
+dimer_file=$2
+n_dimers_to_add=$3
+virion_radius=$4
+ndimers=$5
+
+insert_molecules ${prev_ndimers_file} ${dimer_file} ${n_dimers_to_add} ${virion_radius} 0 25.0 start_${ndimers}.lammps_config
+
+lmp_john -in lammps_new_spherical.in -var CONFIG start_${ndimers}.lammps_config -var NTDNTD_LJEPS 5.0 -var NTDCTD_LJEPS 5.0 -var RANDOMSEED 666 -var SPHERE_RADIUS ${virion_radius} -var NDIMERS ${ndimers}
+
+restart2data end_${ndimers}.restart end_${ndimers}.lammps_config
+
Property changes on: SwiftApps/CMTS/dimers/bin/dimers.sh
___________________________________________________________________
Added: svn:executable
+ *
Modified: SwiftApps/CMTS/dimers/conf/grotthuss.cf
===================================================================
--- SwiftApps/CMTS/dimers/conf/grotthuss.cf 2012-08-23 18:51:16 UTC (rev 5906)
+++ SwiftApps/CMTS/dimers/conf/grotthuss.cf 2012-08-27 07:14:42 UTC (rev 5907)
@@ -7,6 +7,5 @@
provider.staging.pin.swiftfiles=false
use.wrapper.staging=false
-#app insert_molecules=$PWD/../bin/insert_molecules
-#app restart2data=$PWD/../bin/restart2data.sh
+#app dimers=$PWD/../bin/dimers.sh
Modified: SwiftApps/CMTS/dimers/conf/makena.cf
===================================================================
--- SwiftApps/CMTS/dimers/conf/makena.cf 2012-08-23 18:51:16 UTC (rev 5906)
+++ SwiftApps/CMTS/dimers/conf/makena.cf 2012-08-27 07:14:42 UTC (rev 5907)
@@ -7,6 +7,4 @@
provider.staging.pin.swiftfiles=false
use.wrapper.staging=false
-#app insert_molecules=$PWD/../bin/insert_molecules
-#app restart2data=$PWD/../bin/restart2data.sh
-
+#app dimers=$PWD/../bin/dimers.sh
Modified: SwiftApps/CMTS/dimers/dimers.swift
===================================================================
--- SwiftApps/CMTS/dimers/dimers.swift 2012-08-23 18:51:16 UTC (rev 5906)
+++ SwiftApps/CMTS/dimers/dimers.swift 2012-08-27 07:14:42 UTC (rev 5907)
@@ -1,33 +1,30 @@
type file;
-app (file lamps_config_output) insert_molecules (file lamps_config, file dimer, int delta, int v_radius)
+# Dimers wrapper script
+app (file config_out, file restart_out, file trajectory_out) dimers (file previous_file, file lampps_input_file, file dimer, int dimers_to_add, int v_radius, int step)
{
- insert_molecules @lamps_config @dimer delta v_radius 0 25.0 @lamps_config_output;
+ dimers @previous_file @dimer dimers_to_add v_radius step;
}
-app (file output_file) restart2data (file restart_file, file config_file)
-{
- restart2data @restart_file @config_file;
-}
-
-int start_ndimers=20;
-int max_ndimers=70;
+# Parameters
+int start_ndimers=5;
+int max_ndimers=30;
int delta_ndimers=5;
int virion_radius=300;
+# Files
file dimer_file <"dimer_1232.lammps_config">;
file initial_output <"empty.lammps_config">;
-file outputs[];
-outputs[start_ndimers-delta_ndimers] = initial_output;
+file lampps_input <"lammps_new_spherical.in">;
+file lampps_configs[];
-foreach i in [start_ndimers:max_ndimers:delta_ndimers] {
+lampps_configs[start_ndimers-delta_ndimers] = initial_output;
- file molecule_output <single_file_mapper; file=@strcat("end_", i-delta_ndimers, ".lampps_config")>;
- molecule_output = insert_molecules(outputs[i-delta_ndimers], dimer_file, delta_ndimers, virion_radius);
-
- file restart_input <single_file_mapper; file=@strcat("end_", i, ".restart.swift")>;
- file restart_output <single_file_mapper; file=@strcat("end_", i, ".restart")>;
- restart_output = restart2data(restart_input, molecule_output);
-
- outputs[i] = restart_output;
+# Main loop - example of a serial dependency
+foreach i in [start_ndimers:max_ndimers:delta_ndimers] {
+ file config <single_file_mapper; file=@strcat("end_", i, ".lammps_config")>;
+ file restart <single_file_mapper; file=@strcat("end_", i, ".restart")>;
+ file trajectory <single_file_mapper; file=@strcat("traj_", i, ".lammpstrj")>;
+ (config, restart, trajectory) = dimers(lampps_configs[i-delta_ndimers], lampps_input, dimer_file, delta_ndimers, virion_radius, i);
+ lampps_configs[i] = config;
}
Deleted: SwiftApps/CMTS/dimers/input_files/end_20.restart.swift
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Deleted: SwiftApps/CMTS/dimers/input_files/end_25.restart.swift
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Deleted: SwiftApps/CMTS/dimers/input_files/end_30.restart.swift
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Deleted: SwiftApps/CMTS/dimers/input_files/end_35.restart.swift
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Deleted: SwiftApps/CMTS/dimers/input_files/end_40.restart.swift
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Deleted: SwiftApps/CMTS/dimers/input_files/end_45.restart.swift
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Deleted: SwiftApps/CMTS/dimers/input_files/end_50.restart.swift
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Deleted: SwiftApps/CMTS/dimers/input_files/end_55.restart.swift
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Deleted: SwiftApps/CMTS/dimers/input_files/end_60.restart.swift
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Deleted: SwiftApps/CMTS/dimers/input_files/end_65.restart.swift
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Deleted: SwiftApps/CMTS/dimers/input_files/end_70.restart.swift
===================================================================
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Added: SwiftApps/CMTS/dimers/input_files/lammps_new_spherical.in
===================================================================
--- SwiftApps/CMTS/dimers/input_files/lammps_new_spherical.in (rev 0)
+++ SwiftApps/CMTS/dimers/input_files/lammps_new_spherical.in 2012-08-27 07:14:42 UTC (rev 5907)
@@ -0,0 +1,382 @@
+#
+# You need to pass the following variables via the command line:
+#
+# "CONFIG", "NTDNTD_LJEPS", "NTDCTD_LJEPS", "RANDOMSEED", "SPHERE_RADIUS", "NDIMERS"
+#
+# Example:
+#
+# lammps -in <this file> -var CONFIG 1232.lammps_config -var NTDNTD_LJEPS 5.0 -var NTDCTD_LJEPS 5.0 -var RANDOMSEED 666 -var SPHERE_RADIUS x -var NDIMERS y
+#
+
+variable LOGFILE string log.${NDIMERS}
+log ${LOGFILE}
+
+print "Defined variables:"
+print "CONFIG: ${CONFIG}"
+print "RANDOMSEED: ${RANDOMSEED}"
+print "NTDNTD_LJEPS: ${NTDNTD_LJEPS}"
+print "NTDCTD_LJEPS: ${NTDCTD_LJEPS}"
+print "SPHERE_RADIUS: ${SPHERE_RADIUS}"
+print "NDIMERS: ${NDIMERS}"
+
+variable DUMPFILE string traj_${NDIMERS}.lammpstrj
+variable RESTARTFILE string end_${NDIMERS}.restart
+
+variable TSTART equal 310.0
+variable TEND equal 310.0
+variable TDAMP equal 100.0
+
+variable TIMESTEP equal 5.0
+#variable NSTEPS equal 20000000
+#variable DUMPEVERY equal 100000
+variable NSTEPS equal 10000
+variable DUMPEVERY equal 1000
+
+
+units real
+atom_style molecular
+boundary f f f
+
+print "Reading data from ${CONFIG}..."
+read_data ${CONFIG}
+
+# 1 1.000 # 1_1
+# 2 1.000 # 1_2
+# 3 1.000 # 1_3
+# 4 1.000 # 1_4
+# 5 1.000 # 2_1
+# 6 1.000 # 2_2
+# 7 1.000 # 3_1
+# 8 1.000 # 3_2
+# 9 1.000 # 3_3
+# 10 1.000 # 4_1
+# 11 1.000 # 4_2
+# 12 1.000 # 4_3
+# 13 1.000 # 4_4
+# 14 1.000 # 4_5
+# 15 1.000 # 4_6
+# 16 1.000 # 5_1
+# 17 1.000 # 6_1
+# 18 1.000 # 6_2
+# 19 1.000 # 6_3
+# 20 1.000 # 7_1
+# 21 1.000 # 7_2
+# 22 1.000 # 7_3
+# 23 1.000 # 7_4
+# 24 1.000 # 7_5
+# 25 1.000 # 7_6
+# 26 1.000 # AN1
+# 27 1.000 # AN2
+# 28 1.000 # AC1
+# 29 1.000 # AC2
+# 30 1.000 # 8_1
+# 31 1.000 # 8_2
+# 32 1.000 # 8_3
+# 33 1.000 # 8_4
+# 34 1.000 # 9_1
+# 35 1.000 # 9_2
+# 36 1.000 # 9_3
+# 37 1.000 # 9_4
+# 38 1.000 # 10_1
+# 39 1.000 # 10_2
+# 40 1.000 # 10_3
+# 41 1.000 # 11_1
+# 42 1.000 # 11_2
+# 43 1.000 # 12
+
+
+###################################################
+# Bond parameters etc
+###################################################
+bond_style harmonic
+bond_coeff 1 0.1 9.17 # dimer, where necessary
+# NTD-CTD linker constraints; there seem to be relatively insensitive.
+bond_coeff 2 10.0 0.0 # Pivot 1
+bond_coeff 3 10.0 0.0 # Pivot 2
+
+#
+# Improper - parameterized from the CG capsid structure. ~132 degrees
+# reproduces the angle distribution from the CG capsid in simulation pretty well!
+#
+improper_style harmonic
+improper_coeff 1 100.0 132.0
+improper_coeff 2 100.0 132.0
+
+###################################################
+# Ignore forces for beads in the same rigid body
+###################################################
+neigh_modify exclude molecule all
+
+
+###################################################
+# Let's look at what energy we get out of the
+# NTDNTD and NTDCTD interactions during the scale-in,
+# as well as the ghost bonds for the CTD pivot and
+# thw CTD dimer interface bond.
+###################################################
+
+#
+# pairwise interacting types:
+#
+# Although 2_1 -> 3_3 is a smaller distance, 2_2 -> 3_3 is *slightly* more conserved (ie smaller
+# standard deviation / standard error, and smaller absolute gap between lowest and largest distances
+# measured from capsid). It also works *much* better than 2_1 -> 3_3!
+#
+# 4_1 -> 8_3 has a *slightly* smaller average distance and *slightly* smaller spread of values from
+# smallest to largest vs 4_1 -> 8_2 (albeit the standard deviation and standard error are a little
+# larger). I'm not sure there's much of a difference, here; if you plot the distributions using
+# the structural_analysis program, they're basically the same!
+#
+variable tNN1 equal 6 # 2_2
+variable tNN2 equal 9 # 3_3
+variable tNC1 equal 10 # 4_1
+variable tNC2 equal 32 # 8_3
+
+# sites involved in the rotation axis, NTD and CTD
+variable tAN1 equal 26
+variable tAN2 equal 27
+variable tAC1 equal 28
+variable tAC2 equal 29
+
+# dimer bond
+variable tDIM equal 43
+
+#
+# NTD-NTD interaction: 2_1 and 3_3
+#
+group gNN1 type ${tNN1}
+compute NN_pe_v1 gNN1 pe/atom
+compute NN_pe_1 all reduce sum c_NN_pe_v1
+
+group gNN2 type ${tNN2}
+compute NN_pe_v2 gNN2 pe/atom
+compute NN_pe_2 all reduce sum c_NN_pe_v2
+
+group gNN1_NN2 type ${tNN1} ${tNN2}
+compute NN_pe_v gNN1_NN2 pe/atom
+compute NN_pe all reduce sum c_NN_pe_v
+
+#
+# NTD-CTD interaction: 4_1 and 8_2 (or ghost bead!)
+#
+group gNC1 type ${tNC1}
+compute NC_pe_v1 gNC1 pe/atom
+compute NC_pe_1 all reduce sum c_NC_pe_v1
+
+group gNC2 type ${tNC2}
+compute NC_pe_v2 gNC2 pe/atom
+compute NC_pe_2 all reduce sum c_NC_pe_v2
+
+group gNC1_NC2 type ${tNC1} ${tNC2}
+compute NC_pe_v gNC1_NC2 pe/atom
+compute NC_pe all reduce sum c_NC_pe_v
+
+group gNN_NC type ${tNN1} ${tNN2} ${tNC1} ${tNC2}
+compute NN_NC_pe_v gNN_NC pe/atom
+compute NN_NC_pe all reduce sum c_NN_NC_pe_v
+
+#
+# Ghost bond interactions - DI is dimer interface!
+#
+group gAN1_AC1 type ${tAN1} ${tAC1}
+group gAN2_AC2 type ${tAN2} ${tAC2}
+group gPivot type ${tAN1} ${tAC1} ${tAN2} ${tAC2}
+group gDI type ${tDIM}
+
+compute A1_be_v gAN1_AC1 pe/atom bond
+compute A1_be all reduce sum c_A1_be_v
+
+compute A2_be_v gAN2_AC2 pe/atom bond
+compute A2_be all reduce sum c_A2_be_v
+
+compute Pivot_be_v gPivot pe/atom bond
+compute Pivot_be all reduce sum c_Pivot_be_v
+
+compute DI_be_v gDI pe/atom bond
+compute DI_be all reduce sum c_DI_be_v
+
+#
+# check what weird-ass method lammps uses for the improper dihedral calculation
+#
+#group gimp1 id 25 27 26 30
+group gimp1 type 25 27 26 30
+compute imp1 gimp1 improper/local chi
+compute imp1_min all reduce min c_imp1
+compute imp1_ave all reduce ave c_imp1
+compute imp1_max all reduce max c_imp1
+
+
+# special thermo output for scale-in; list temperature, bond energy, nonbonded energy, then specific NTD-NTD, NTD-CTD and NTDNTD+NTDCTD energy
+thermo_style custom step cpu temp evdwl c_NN_pe c_NC_pe c_NN_NC_pe ebond c_A1_be c_A2_be c_Pivot_be c_DI_be c_imp1_min c_imp1_ave c_imp1_max
+
+
+###################################################
+# some system info
+###################################################
+thermo ${DUMPEVERY}
+dump 1 all custom ${DUMPEVERY} ${DUMPFILE} id mol type x y z
+dump_modify 1 sort id
+timestep ${TIMESTEP}
+
+
+###################################################
+# Fixes, initial velocity distribution
+###################################################
+# Nose-Hoover
+fix 1 all rigid/nvt molecule temp ${TSTART} ${TEND} ${TDAMP} tparam 10 6 3
+
+# sphere constraint
+fix 2 all wall/harmonicsphericaljohn xhi ${SPHERE_RADIUS} 0.05 1.0 ${SPHERE_RADIUS} units box
+
+# Langevin
+#fix 1 all rigid/nve molecule
+#fix 2 all langevin ${TSTART} ${TEND} ${TDAMP} ${RANDOMSEED}
+
+velocity all create ${TSTART} ${RANDOMSEED} mom yes rot yes dist gaussian
+
+
+#############################################################
+# Nonbonded: Morse (pure exclusion) & LJ (attractive wells) #
+#############################################################
+# Notes:
+# 1. Lammps uses the star notation for "all types", but it's
+# implicit that the second type in the pair_coeff line is
+# larger than the first; we therefore have to use the star
+# both "before" and "after" the global type interaction.
+# This is why eg the ghost types have both "x *" and
+# "* x" when we set them to have no excluded volume effect
+# with any other type in the system.
+#############################################################
+#pair_style hybrid lj/cut 25.0 lj/john 12.0 morse 12.0
+pair_style hybrid lj/cut 25.0 morse 12.0
+# -- Morse params -------------------------------------------
+variable MORSE_D0 equal 0.0001
+variable MORSE_ALPHA equal 4.5
+
+# -- default size excluded radius ----
+pair_coeff * * morse ${MORSE_D0} ${MORSE_ALPHA} 12.0 12.0
+
+# -- raw output from capsid analysis, independent NTD and CTD superpositions ----
+pair_coeff 1 1 morse ${MORSE_D0} ${MORSE_ALPHA} 9.891 9.891 # 1_1 1_1: 9.891 10.705 10.755
+pair_coeff 1 2 morse ${MORSE_D0} ${MORSE_ALPHA} 9.565 9.565 # 1_1 1_2: 9.565 10.301 10.347
+pair_coeff 1 3 morse ${MORSE_D0} ${MORSE_ALPHA} 11.366 11.366 # 1_1 1_3: 11.366 11.935 11.971
+pair_coeff 1 6 morse ${MORSE_D0} ${MORSE_ALPHA} 10.178 10.178 # 1_1 2_2: 10.178 10.187 10.188
+pair_coeff 2 2 morse ${MORSE_D0} ${MORSE_ALPHA} 11.196 11.196 # 1_2 1_2: 11.196 11.197 11.198
+pair_coeff 2 3 morse ${MORSE_D0} ${MORSE_ALPHA} 11.207 11.207 # 1_2 1_3: 11.207 11.207 11.209
+pair_coeff 2 6 morse ${MORSE_D0} ${MORSE_ALPHA} 11.657 11.657 # 1_2 2_2: 11.657 11.883 11.897
+pair_coeff 3 29 morse ${MORSE_D0} ${MORSE_ALPHA} 11.247 11.247 # 1_3 AC2: 11.247 11.247 11.247
+pair_coeff 4 29 morse ${MORSE_D0} ${MORSE_ALPHA} 10.586 10.586 # 1_4 AC2: 10.586 11.428 11.796
+pair_coeff 5 8 morse ${MORSE_D0} ${MORSE_ALPHA} 10.814 10.814 # 2_1 3_2: 10.814 10.862 11.644
+pair_coeff 5 9 morse ${MORSE_D0} ${MORSE_ALPHA} 7.744 7.744 # 2_1 3_3: 7.744 7.773 8.243
+pair_coeff 5 29 morse ${MORSE_D0} ${MORSE_ALPHA} 7.128 7.128 # 2_1 AC2: 7.128 8.862 11.920
+pair_coeff 5 33 morse ${MORSE_D0} ${MORSE_ALPHA} 10.876 10.876 # 2_1 8_4: 10.876 11.619 11.997
+pair_coeff 6 8 morse ${MORSE_D0} ${MORSE_ALPHA} 10.393 10.393 # 2_2 3_2: 10.393 10.456 11.492
+pair_coeff 6 9 morse ${MORSE_D0} ${MORSE_ALPHA} 9.675 9.675 # 2_2 3_3: 9.675 9.704 10.159
+pair_coeff 8 29 morse ${MORSE_D0} ${MORSE_ALPHA} 9.672 9.672 # 3_2 AC2: 9.672 11.430 11.997
+pair_coeff 9 27 morse ${MORSE_D0} ${MORSE_ALPHA} 9.945 9.945 # 3_3 AN2: 9.945 9.967 10.322
+pair_coeff 9 29 morse ${MORSE_D0} ${MORSE_ALPHA} 6.143 6.143 # 3_3 AC2: 6.143 8.920 11.839
+pair_coeff 9 33 morse ${MORSE_D0} ${MORSE_ALPHA} 10.806 10.806 # 3_3 8_4: 10.806 11.524 11.972
+pair_coeff 10 26 morse ${MORSE_D0} ${MORSE_ALPHA} 11.109 11.109 # 4_1 AN1: 11.109 11.128 11.431
+pair_coeff 10 27 morse ${MORSE_D0} ${MORSE_ALPHA} 9.080 9.080 # 4_1 AN2: 9.080 9.083 9.117
+pair_coeff 10 28 morse ${MORSE_D0} ${MORSE_ALPHA} 7.985 7.985 # 4_1 AC1: 7.985 10.524 11.996
+pair_coeff 10 29 morse ${MORSE_D0} ${MORSE_ALPHA} 2.501 2.501 # 4_1 AC2: 2.501 8.595 10.808
+pair_coeff 10 30 morse ${MORSE_D0} ${MORSE_ALPHA} 8.581 8.581 # 4_1 8_1: 8.581 10.780 11.991
+pair_coeff 10 31 morse ${MORSE_D0} ${MORSE_ALPHA} 5.397 5.397 # 4_1 8_2: 5.397 7.996 10.379
+pair_coeff 10 32 morse ${MORSE_D0} ${MORSE_ALPHA} 5.100 5.100 # 4_1 8_3: 5.100 7.925 9.861
+pair_coeff 10 33 morse ${MORSE_D0} ${MORSE_ALPHA} 5.196 5.196 # 4_1 8_4: 5.196 9.826 11.658
+pair_coeff 10 41 morse ${MORSE_D0} ${MORSE_ALPHA} 10.110 10.110 # 4_1 11_1: 10.110 11.413 11.999
+pair_coeff 10 42 morse ${MORSE_D0} ${MORSE_ALPHA} 11.606 11.606 # 4_1 11_2: 11.606 11.835 11.995
+pair_coeff 11 27 morse ${MORSE_D0} ${MORSE_ALPHA} 11.301 11.301 # 4_2 AN2: 11.301 11.308 11.409
+pair_coeff 11 28 morse ${MORSE_D0} ${MORSE_ALPHA} 10.782 10.782 # 4_2 AC1: 10.782 11.744 12.000
+pair_coeff 11 29 morse ${MORSE_D0} ${MORSE_ALPHA} 4.749 4.749 # 4_2 AC2: 4.749 10.138 11.996
+pair_coeff 11 30 morse ${MORSE_D0} ${MORSE_ALPHA} 11.415 11.415 # 4_2 8_1: 11.415 11.719 11.973
+pair_coeff 11 31 morse ${MORSE_D0} ${MORSE_ALPHA} 8.439 8.439 # 4_2 8_2: 8.439 11.119 11.999
+pair_coeff 11 32 morse ${MORSE_D0} ${MORSE_ALPHA} 8.333 8.333 # 4_2 8_3: 8.333 11.011 11.999
+pair_coeff 11 33 morse ${MORSE_D0} ${MORSE_ALPHA} 8.698 8.698 # 4_2 8_4: 8.698 11.123 11.998
+pair_coeff 11 41 morse ${MORSE_D0} ${MORSE_ALPHA} 8.066 8.066 # 4_2 11_1: 8.066 10.726 12.000
+pair_coeff 11 42 morse ${MORSE_D0} ${MORSE_ALPHA} 11.011 11.011 # 4_2 11_2: 11.011 11.622 11.998
+pair_coeff 12 29 morse ${MORSE_D0} ${MORSE_ALPHA} 9.835 9.835 # 4_3 AC2: 9.835 11.080 11.989
+pair_coeff 12 41 morse ${MORSE_D0} ${MORSE_ALPHA} 9.931 9.931 # 4_3 11_1: 9.931 11.300 11.999
+pair_coeff 24 29 morse ${MORSE_D0} ${MORSE_ALPHA} 10.115 10.115 # 7_5 AC2: 10.115 11.358 12.000
+pair_coeff 24 33 morse ${MORSE_D0} ${MORSE_ALPHA} 10.974 10.974 # 7_5 8_4: 10.974 11.572 11.997
+pair_coeff 24 41 morse ${MORSE_D0} ${MORSE_ALPHA} 10.207 10.207 # 7_5 11_1: 10.207 11.419 11.992
+pair_coeff 24 42 morse ${MORSE_D0} ${MORSE_ALPHA} 9.468 9.468 # 7_5 11_2: 9.468 11.169 11.998
+pair_coeff 25 28 morse ${MORSE_D0} ${MORSE_ALPHA} 11.525 11.525 # 7_6 AC1: 11.525 11.777 11.982
+pair_coeff 25 29 morse ${MORSE_D0} ${MORSE_ALPHA} 9.917 9.917 # 7_6 AC2: 9.917 11.265 11.994
+pair_coeff 25 30 morse ${MORSE_D0} ${MORSE_ALPHA} 10.548 10.548 # 7_6 8_1: 10.548 11.533 11.977
+pair_coeff 25 33 morse ${MORSE_D0} ${MORSE_ALPHA} 9.307 9.307 # 7_6 8_4: 9.307 10.121 11.997
+pair_coeff 25 41 morse ${MORSE_D0} ${MORSE_ALPHA} 10.508 10.508 # 7_6 11_1: 10.508 11.500 11.989
+pair_coeff 25 42 morse ${MORSE_D0} ${MORSE_ALPHA} 8.144 8.144 # 7_6 11_2: 8.144 10.663 11.985
+pair_coeff 26 28 morse ${MORSE_D0} ${MORSE_ALPHA} 0.277 0.277 # AN1 AC1: 0.277 1.693 4.228
+pair_coeff 26 29 morse ${MORSE_D0} ${MORSE_ALPHA} 8.840 8.840 # AN1 AC2: 8.840 10.660 11.997
+pair_coeff 26 30 morse ${MORSE_D0} ${MORSE_ALPHA} 9.190 9.190 # AN1 8_1: 9.190 11.163 11.999
+pair_coeff 26 31 morse ${MORSE_D0} ${MORSE_ALPHA} 5.725 5.725 # AN1 8_2: 5.725 8.001 10.884
+pair_coeff 26 32 morse ${MORSE_D0} ${MORSE_ALPHA} 2.296 2.296 # AN1 8_3: 2.296 4.609 7.720
+pair_coeff 26 33 morse ${MORSE_D0} ${MORSE_ALPHA} 4.298 4.298 # AN1 8_4: 4.298 6.119 8.959
+pair_coeff 26 34 morse ${MORSE_D0} ${MORSE_ALPHA} 7.771 7.771 # AN1 9_1: 7.771 10.421 11.992
+pair_coeff 26 35 morse ${MORSE_D0} ${MORSE_ALPHA} 5.446 5.446 # AN1 9_2: 5.446 8.505 11.909
+pair_coeff 26 36 morse ${MORSE_D0} ${MORSE_ALPHA} 5.025 5.025 # AN1 9_3: 5.025 8.167 11.994
+pair_coeff 26 37 morse ${MORSE_D0} ${MORSE_ALPHA} 5.987 5.987 # AN1 9_4: 5.987 9.062 11.969
+pair_coeff 26 43 morse ${MORSE_D0} ${MORSE_ALPHA} 3.816 3.816 # AN1 12: 3.816 7.256 11.981
+pair_coeff 27 28 morse ${MORSE_D0} ${MORSE_ALPHA} 6.778 6.778 # AN2 AC1: 6.778 9.066 10.948
+pair_coeff 27 29 morse ${MORSE_D0} ${MORSE_ALPHA} 0.422 0.422 # AN2 AC2: 0.422 2.216 7.719
+pair_coeff 27 31 morse ${MORSE_D0} ${MORSE_ALPHA} 11.120 11.120 # AN2 8_2: 11.120 11.821 11.999
+pair_coeff 27 32 morse ${MORSE_D0} ${MORSE_ALPHA} 6.050 6.050 # AN2 8_3: 6.050 7.306 9.818
+pair_coeff 27 33 morse ${MORSE_D0} ${MORSE_ALPHA} 2.330 2.330 # AN2 8_4: 2.330 4.398 7.000
+pair_coeff 27 34 morse ${MORSE_D0} ${MORSE_ALPHA} 10.795 10.795 # AN2 9_1: 10.795 11.697 11.975
+pair_coeff 27 35 morse ${MORSE_D0} ${MORSE_ALPHA} 11.673 11.673 # AN2 9_2: 11.673 11.673 11.673
+pair_coeff 27 43 morse ${MORSE_D0} ${MORSE_ALPHA} 10.447 10.447 # AN2 12: 10.447 11.613 11.965
+pair_coeff 30 40 morse ${MORSE_D0} ${MORSE_ALPHA} 9.753 9.753 # 8_1 10_3: 9.753 11.067 11.975
+pair_coeff 34 34 morse ${MORSE_D0} ${MORSE_ALPHA} 4.337 4.337 # 9_1 9_1: 4.337 9.883 10.595
+pair_coeff 34 35 morse ${MORSE_D0} ${MORSE_ALPHA} 6.685 6.685 # 9_1 9_2: 6.685 6.686 6.687
+pair_coeff 34 36 morse ${MORSE_D0} ${MORSE_ALPHA} 9.967 9.967 # 9_1 9_3: 9.967 9.968 9.969
+pair_coeff 34 43 morse ${MORSE_D0} ${MORSE_ALPHA} 7.367 7.367 # 9_1 12: 7.367 11.092 11.571
+pair_coeff 35 35 morse ${MORSE_D0} ${MORSE_ALPHA} 6.424 6.424 # 9_2 9_2: 6.424 6.425 6.426
+pair_coeff 35 36 morse ${MORSE_D0} ${MORSE_ALPHA} 7.873 7.873 # 9_2 9_3: 7.873 7.874 7.875
+pair_coeff 35 37 morse ${MORSE_D0} ${MORSE_ALPHA} 11.212 11.212 # 9_2 9_4: 11.212 11.213 11.214
+pair_coeff 35 43 morse ${MORSE_D0} ${MORSE_ALPHA} 5.309 5.309 # 9_2 12: 5.309 10.529 11.200
+pair_coeff 36 36 morse ${MORSE_D0} ${MORSE_ALPHA} 6.831 6.831 # 9_3 9_3: 6.831 6.832 6.833
+pair_coeff 36 37 morse ${MORSE_D0} ${MORSE_ALPHA} 8.652 8.652 # 9_3 9_4: 8.652 8.653 8.654
+pair_coeff 36 43 morse ${MORSE_D0} ${MORSE_ALPHA} 5.640 5.640 # 9_3 12: 5.640 10.765 11.424
+pair_coeff 37 37 morse ${MORSE_D0} ${MORSE_ALPHA} 8.340 8.340 # 9_4 9_4: 8.340 8.341 8.342
+pair_coeff 37 43 morse ${MORSE_D0} ${MORSE_ALPHA} 8.910 8.910 # 9_4 12: 8.910 8.911 8.912
+pair_coeff 38 40 morse ${MORSE_D0} ${MORSE_ALPHA} 9.360 9.360 # 10_1 10_3: 9.360 10.984 11.983
+pair_coeff 39 39 morse ${MORSE_D0} ${MORSE_ALPHA} 9.299 9.299 # 10_2 10_2: 9.299 11.228 12.000
+pair_coeff 39 40 morse ${MORSE_D0} ${MORSE_ALPHA} 6.916 6.916 # 10_2 10_3: 6.916 10.645 11.995
+pair_coeff 39 42 morse ${MORSE_D0} ${MORSE_ALPHA} 9.311 9.311 # 10_2 11_2: 9.311 11.030 11.989
+pair_coeff 40 40 morse ${MORSE_D0} ${MORSE_ALPHA} 4.327 4.327 # 10_3 10_3: 4.327 9.538 11.995
+pair_coeff 40 41 morse ${MORSE_D0} ${MORSE_ALPHA} 8.798 8.798 # 10_3 11_1: 8.798 10.732 12.000
+pair_coeff 40 42 morse ${MORSE_D0} ${MORSE_ALPHA} 5.234 5.234 # 10_3 11_2: 5.234 9.733 11.998
+pair_coeff 41 41 morse ${MORSE_D0} ${MORSE_ALPHA} 8.882 8.882 # 11_1 11_1: 8.882 10.866 11.874
+pair_coeff 41 42 morse ${MORSE_D0} ${MORSE_ALPHA} 8.214 8.214 # 11_1 11_2: 8.214 10.925 11.993
+pair_coeff 42 42 morse ${MORSE_D0} ${MORSE_ALPHA} 8.702 8.702 # 11_2 11_2: 8.702 10.987 11.983
+pair_coeff 43 43 morse ${MORSE_D0} ${MORSE_ALPHA} 5.173 5.173 # 12 12: 5.173 8.727 9.183
+
+# -- ghost sites have no morse interaction with anything ----
+pair_coeff 26 * morse ${MORSE_D0} ${MORSE_ALPHA} 0.0 0.0
+pair_coeff * 26 morse ${MORSE_D0} ${MORSE_ALPHA} 0.0 0.0
+pair_coeff 27 * morse ${MORSE_D0} ${MORSE_ALPHA} 0.0 0.0
+pair_coeff * 27 morse ${MORSE_D0} ${MORSE_ALPHA} 0.0 0.0
+pair_coeff 28 * morse ${MORSE_D0} ${MORSE_ALPHA} 0.0 0.0
+pair_coeff * 28 morse ${MORSE_D0} ${MORSE_ALPHA} 0.0 0.0
+pair_coeff 29 * morse ${MORSE_D0} ${MORSE_ALPHA} 0.0 0.0
+pair_coeff * 29 morse ${MORSE_D0} ${MORSE_ALPHA} 0.0 0.0
+pair_coeff 43 * morse ${MORSE_D0} ${MORSE_ALPHA} 0.0 0.0
+pair_coeff * 43 morse ${MORSE_D0} ${MORSE_ALPHA} 0.0 0.0
+
+# from independent NTD and CTD superpositions onto hexs and pents
+#pair_coeff ${tNN1} ${tNN2} lj/cut ${NTDNTD_LJEPS} 6.925
+#pair_coeff ${tNC1} ${tNC2} lj/cut ${NTDCTD_LJEPS} 7.39
+
+# from superposition onto capsid
+#pair_coeff ${tNN1} ${tNN2} lj/cut ${NTDNTD_LJEPS} 7.27
+#pair_coeff ${tNC1} ${tNC2} lj/cut ${NTDCTD_LJEPS} 8.3
+
+pair_coeff ${tNN1} ${tNN2} lj/cut ${NTDNTD_LJEPS} 8.65 # for 2_2, 3_3 - most conserved NTD-NTD distance from capsid!
+pair_coeff ${tNC1} ${tNC2} lj/cut ${NTDCTD_LJEPS} 7.39 # for 4_1, 8_3 - most conserved NTD-CTD distance from capsid!
+
+pair_modify shift yes
+
+run ${NSTEPS}
+
+write_restart ${RESTARTFILE}
\ No newline at end of file
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