Water is boiling with namd and charmm

From: DimitryASuplatov (genesup_at_gmail.com)
Date: Mon Apr 13 2009 - 09:27:54 CDT

Hello,

I am running 10ns molecular dynamics simulation starting from 0K, then
heating to 300K, then followed by 10 ns of free dynamics at 300K.
At some point I noticed water "boiling" in the cell - huge bubbles
appeared in the water. I guess this happened since I did not set the
constant pressure so my system remained at constant volume.
Am I correct?
I have rounded the cellBasisVector coordinates (lets say, from 108,7 to
109). Could this be the cause?
Should I use constant pressure at next simmulation? Configuration file
is below.

Thanks for your time.
SDA

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

# STRMB in a Water Box

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

structure ./strmb.s.charmm.psf
coordinates ./strmb.s.charmm.pdb

set start_temperature 0
set hold_temperature 300
set outputname strmb.md.charmm.namd

firsttimestep 0

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

# Input
paraTypeCharmm on
parameters ./par_all27_prot_lipid.inp
temperature $start_temperature

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 15.
switching on
switchdist 10.

# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinTemp 0
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinHydrogen off ;# don't couple langevin bath to hydrogens

# Periodic Boundary Conditions
cellBasisVector1 109 0. 0.
cellBasisVector2 0. 103 0.
cellBasisVector3 0. 0 106.
cellOrigin 63.87940979 13.3578186035 32.2524185181

wrapAll on

#PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 125
PMEGridSizeY 125
PMEGridSizeZ 125

# Output
outputName $outputname

restartfreq 10000
dcdfreq 2000
xstFreq 2000
outputEnergies 2000
outputPressure 10000

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

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

# Minimization
minimize 5000

#Heat
for { set TEMP $start_temperature } { $TEMP < $hold_temperature } { incr
TEMP 25 } {
        langevinTemp $TEMP
        reassignTemp $TEMP
             run 5000
}

reassignTemp $hold_temperature
langevinTemp $hold_temperature
run 5000000

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