System expands: CCL4 simulation; NPT(Langevin Piston)

From: satya work (satya.work_at_gmail.com)
Date: Tue Apr 28 2009 - 16:10:32 CDT

Dear NAMD users,

I have been encountering a rather strange problem with a simple NPT
simulation of CCL4 molecules.

I have used OPLS parameters for the CCL4 simulation and had
accidentally given Rmin values for C and Cl instead Rmin/2 in the
parameter file. The system runs but does not reproduce the correct
density.

After realising the above mistake, I give the correct values LJ values
of C & Cl (Rmin/2), and not changing any other simulation conditions,
the system size doubles and stays put !!

The initial coordinates of CCL4 are at rather low density, so this
expansion of the box for the correct values of Rmin/2 is confusing me.

The Configuration file is attached below:
--------------------------------------------------------
structure ./ccl4_namd_0.5k.psf
coordinates ./ccl4_namd_0.5k.pdb
set previous CCL4-run1
set current CCL4-run1
#bincoordinates ./$previous.restart.coor
#binvelocities ./$previous.restart.vel
#extendedSystem ./$previous.restart.xsc
set temperature 298
set outputname ./$current

firsttimestep 0

#############################################################
## SIMULATION PARAMETERS ##
#############################################################

# Input
paraTypeCharmm on
parameters ./par_all27_ccl4_cholesterol_ethanol.prm
temperature $temperature
#temperature 5
#reassignFreq 1000
#reassignTemp 5
#reassignIncr 5
#reassignHold 310.0

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 15.0
margin 4.0

# Integrator Parameters
# fullElectFrequency*timestep <=4.0
# stable time steps:
# with rigidBonds=all: electro:6fs;short-rangeNB:2fs;bonded:2fs
# otherwise : 2fs 2fs 1fs
timestep 2.0 ;# 2fs/step
rigidBonds all ;# Needed for 2fs steps
useSettle on
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

# Constant Temperature Control
langevin off ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens

#temperature coupling for temperature coupling
tCouple on
tCoupleTemp $temperature

# Periodic Boundary Conditions
# center of the periodic box; NOT ORIGIN!!!
cellBasisVector1 102 0. 0.
cellBasisVector2 0. 102 0.
cellBasisVector3 0. 0. 102
cellOrigin 0. 0. 0.

wrapAll on

# PME (for full-system periodic electrostatics)
# multiples of 2,3,5 & >=dimensions above
PME yes
PMEGridSizeX 120
PMEGridSizeY 120
PMEGridSizeZ 120

# 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.
langevinPistonDecay 50.
langevinPistonTemp $temperature

# Output
outputName $outputname

restartfreq 500 ;# 500steps = every 1ps
dcdfreq 500
xstFreq 500
outputEnergies 500
outputPressure 500

#############################################################
## EXECUTION SCRIPT ##
#############################################################

# Minimization
minimize 1000
reinitvels $temperature

run 1000000 ;#

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