From: Bikan Tan (btan_at_ncsu.edu)
Date: Mon Jan 14 2013 - 11:01:06 CST
Hi all,
I am doing a simulation with DNA surrounded by a shell of water in a big
cell box with vacuum padding with periodic boundary condition. I notice
that the cell size is shrinking as the simulation goes. So, eventually the
water shell changes its shape from a sphere into a cubic water box. My
question is how to keep the cell size the same as the simulation goes.
I attached my input parameters for your convenience.
Thank you very much for your time and help.
Best regards
Bikan
#############################################################
## JOB DESCRIPTION ##
#############################################################
# Minimization and Equilibration of
# Ubiquitin in a Water Box
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
set basefilename system_cions_4GC.pas_ws_autoionize
structure ./$basefilename.psf
coordinates ./$basefilename.pdb
set temperature 290
# Continuing a job from the restart
files
# Modify this line on restart
set RESTART 11139000
set NEW 4
set OLD 3
# Modify this line on restart
set outputname ./Restart_$NEW/$basefilename
file mkdir Restart_$NEW
if {$RESTART} {
# Modify this line on restart
set inputname ./Restart_$OLD/$basefilename.restart
binCoordinates $inputname.coor
binVelocities $inputname.vel
extendedSystem $inputname.xsc
}
firsttimestep $RESTART
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters ./par_all27_prot_na.inp
if { $RESTART == 0 } {
temperature $temperature
}
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 13.5
# Integrator Parameters
timestep 0.5 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Periodic Boundary Conditions
if {$RESTART == 0} {
cellBasisVector1 144 0.0 0.0
cellBasisVector2 0.0 144 0.0
cellBasisVector3 0.0 0.0 144
cellOrigin -4.364318370819092 2.1020102500915527 1.3885084390640259
}
wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
#PMEGridSpacing 1.0
#manual grid definition
PMEGridSizeX 160
PMEGridSizeY 160
PMEGridSizeZ 160
# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.0
langevinPistonDecay 50.0
langevinPistonTemp $temperature
# Output
outputName $outputname
restartfreq 1000 ;# 500steps = every 1ps
dcdfreq 1000
xstFreq 1000
outputEnergies 500
outputPressure 500
#############################################################
## EXTRA PARAMETERS ##
#############################################################
fixedAtoms on
fixedAtomsForces off
fixedAtomsCol B
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
# Minimization
if {$RESTART == 0 } {
minimize 5000
reinitvels $temperature
}
run 8000000 ;# 4ns
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