From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Jan 15 2013 - 00:39:59 CST
Hi,
of course the box shrinks if you tell namd to equilibrate pressure in a cell
containing vacuum to 1 athmosphere, that's what it's meant for. To keep the
vacuum, set the LangevinPiston parameter to off.
Please try to answer such questions by using the manual. It would have told
you the meanings of the keywords in your script easily.
Good luck
Norman Geist.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Bikan Tan
Gesendet: Montag, 14. Januar 2013 18:01
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: DNA surrounded by a shell of water in a big box with vacuum
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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