[Swift-commit] r5932 - SwiftApps/CMTS/scaling/input_files

[davidk at ci.uchicago.edu]

Author: davidk
Date: 2012-09-18 14:33:39 -0500 (Tue, 18 Sep 2012)
New Revision: 5932

Added:
   SwiftApps/CMTS/scaling/input_files/h0_eq.conf
Log:
namd config file


Added: SwiftApps/CMTS/scaling/input_files/h0_eq.conf
===================================================================
--- SwiftApps/CMTS/scaling/input_files/h0_eq.conf	                        (rev 0)
+++ SwiftApps/CMTS/scaling/input_files/h0_eq.conf	2012-09-18 19:33:39 UTC (rev 5932)
@@ -0,0 +1,109 @@
+############################################################
+## JOB DESCRIPTION                                         ##
+#############################################################
+
+# Minimization and equilibration of waters with 
+# protein held fixed to reduce artifacts
+
+set WORK	   _WORK_
+
+#############################################################
+## ADJUSTABLE PARAMETERS                                   ##
+#############################################################
+
+structure          $WORK/h0_solvion.psf
+coordinates        $WORK/h0_solvion.pdb
+
+#############################################################
+# Output Names                                             ##
+#############################################################
+set basename       h0_eq.JOB
+outputName         $WORK/OUT/$basename
+DCDfile            $WORK/OUT/$basename.dcd
+restartname        $WORK/RESTART/$basename.restart
+
+# Initial temperature
+set temperature    310
+
+# Continuing a job from the restart files
+if {1} {
+set inputname      h0_eq.0 
+binCoordinates     $WORK/RESTART/$inputname.restart.coor
+binVelocities      $WORK/RESTART/$inputname.restart.vel  
+extendedSystem     $WORK/RESTART/$inputname.restart.xsc
+}
+
+firsttimestep 	  0  		      
+
+#############################################################
+## SIMULATION PARAMETERS                                   ##
+#############################################################
+
+# Input
+paraTypeCharmm      on
+parameters          $WORK/par_all22_prot.inp
+
+# Periodic Boundary Conditions from extended system cell (.xsc) 
+wrapWater           on
+wrapAll             on
+
+
+# Force-Field Parameters
+exclude             scaled1-4
+1-4scaling          1.0
+cutoff              12.0
+switching           on
+switchdist          10.0
+pairlistdist        13.5
+
+# Integrator Parameters
+timestep            2.0  ;# 2fs/step
+rigidBonds          all  ;# needed for 2fs steps
+nonbondedFreq       2
+fullElectFrequency  2
+stepspercycle       20
+
+PME                 yes
+PMEPencils          16
+PMETolerance     1.0e-6
+PMEInterpOrder   4
+PMEGridSpacing   1.0
+
+# Constant Temperature Control
+langevin            on    ;# do langevin dynamics
+langevinDamping     .5     ;# damping coefficient (gamma) of 5/ps
+langevinTemp        $temperature
+langevinHydrogen    off
+
+# Constant Pressure Control (variable volume)
+if {0} {
+useGroupPressure      yes ;# needed for 2fs steps
+useFlexibleCell       no  ;# no for water box, yes for membrane
+useConstantArea       no  ;# no for water box, yes for membrane
+
+langevinPiston        on
+langevinPistonTarget  1.01325 ;#  in bar -> 1 atm
+langevinPistonPeriod  2000.0
+langevinPistonDecay   2000.0
+langevinPistonTemp    $temperature
+}
+
+restartfreq        20     ;# 1000steps =  every 2ps
+dcdfreq            20
+xstFreq            20
+outputEnergies     20
+outputPressure     20
+
+
+#############################################################
+## EXTRA PARAMETERS                                        ##
+#############################################################
+
+# Put here any custom parameters that are specific to 
+# this job (e.g., SMD, TclForces, etc...)
+
+#############################################################
+## EXECUTION SCRIPT                                        ##
+#############################################################
+
+run 5000