From: snoze pa (snoze.pa_at_gmail.com)
Date: Fri Apr 15 2011 - 13:23:53 CDT
Dear NAMD users,
I am running a NAMD simulation. The PMEGridSize and cellBasisVector are
correctly assigned. I can see clearly the periodic cell in VMD. But when I
run the simulation, after the simulation I found gap between period cell in
z direction. I can see large gap using vmd in z direction. It appears to me
that the cells are increasing in Z direction.
Here is example for two periodic cell before simulation in z direction.
there is only one gap in Z Direction denoted by -
XXX-XXX
XXX-XXX
XXX-XXX
But after simulation it become too large in Z direction and I can see from
VMD periodic cell option.
XXX------XXX
XXX------XXX
XXX------XXX
Why it is happening. It is not good. After simulation the periodic cells
should be in contact with each other
Thank you for your help.
Following is the script I am using:
set MOL solvatedProtein
structure ${MOL}_ionised.psf
coordinates ${MOL}_ionised.pdb
outputname ${MOL}_ionised_min
set temperature 300
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters par_all27_prot_lipid.inp
temperature $temperature
if {1} {
cellBasisVector1 115 0. 0.
cellBasisVector2 0. 95.243 0.
cellBasisVector3 0. 0. 102.67200
cellOrigin 14.1914 13.8195 51.2961692
}
wrapWater on
wrapAll on
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5
# Integrator Parameters
timestep 1.0 ;# 1fs/step
rigidBonds all
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20
#PME (for full-system periodic electrostatics)
if {1} {
PME yes
PMEGridSizeX 120
PMEGridSizeY 100
PMEGridSizeZ 108
}
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
# 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 200.
langevinPistonDecay 50.
langevinPistonTemp $temperature
}
restartfreq 1000
dcdfreq 1000
xstFreq 1000
outputEnergies 1000
outputPressure 1000
constraints on
consexp 2
consref solvated_ionisedProtein.pdb
conskfile solvated_ionisedProtein.cnst
conskcol B
margin 3
# Minimization
if {1} {
minimize 10000
reinitvels $temperature
}
run 500000
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