water box deformation

From: ais_at_fh.huji.ac.il
Date: Wed Feb 09 2011 - 09:47:27 CST

hi,
i'm running an npt simulation with periodic boundary conditions.
i notice that as the simulation advances, the water box collapses into a
shape similar to a sphere.
the current run is a restart over a 40ps minimization that i ran earlier
on the system.
in the minimization script i specified the periodic cell dimensions but
in the restart run i didn't since i gave a restart xsc file.
- could anyone suggest an explanation for this phenomenon & point out
what i've done wrong?
- could this be related to the 'periodic cell has become too small for
original patch grid...' error message that i get?

i attach my restart conf file below.
thanks, Ai

#############################################################
## JOB DESCRIPTION ##
#############################################################

#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################

structure 02_04_1zgoa_ion.psf
coordinates 02_04_1zgoa_ion.pdb
outputName 10_1zgoa

set temperature 310

# Continuing a job from the restart files
if {1} {
set inputname 07_1zgoa
binCoordinates $inputname.restart.coor
binVelocities $inputname.restart.vel ;# remove the "temperature"
entry if you use this!
extendedSystem $inputname.xsc
}

firsttimestep 40000

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

# Input
paraTypeCharmm on
parameters par_all27_prot_lipid_ai.inp

# NOTE: Do not set the initial velocity temperature if you
# have also specified a .vel restart file!
# temperature $temperature
 

# Periodic Boundary conditions
# NOTE: Do not set the periodic cell basis if you have also
# specified an .xsc restart file!
if {0} {
cellBasisVector1 82.67 0. 0.
cellBasisVector2 0. 88.12 0.
cellBasisVector3 0. 0 92.44
cellOrigin 19.00 -14.80 38.19
}
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 ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

#PME (for full-system periodic electrostatics)
if {1} {
PME yes
PMEGridSizeX 90
PMEGridSizeY 90
PMEGridSizeZ 96
}

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen no ;# don't couple langevin bath to hydrogens

# Constant Pressure Control (variable volume)
if {1} {
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 500 ;# 500steps = every 1ps
dcdfreq 500
xstFreq 500
outputEnergies 100
outputPressure 100

# Fixed Atoms Constraint (set PDB beta-column to 1)
if {0} {
fixedAtoms on
fixedAtomsFile myfixedatoms.pdb
fixedAtomsCol B
}

# IMD Settings (can view sim in VMD)
if {0} {
IMDon on
IMDport 3000 ;# port number (enter it in VMD)
IMDfreq 1 ;# send every 1 frame
IMDwait no ;# wait for VMD to connect before running?
}

#############################################################
## EXTRA PARAMETERS ##
#############################################################

# Put here any custom parameters that are specific to
# this job (e.g., SMD, TclForces, etc...)

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

# Minimization
if {0} {
minimize 40000 ;#40 ps
reinitvels $temperature
}

run 1000000 ;# 1000ps=1ns

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