Problem with SPC/E water simulation

From: Davide Vanzo/FS/VCU (dvanzo_at_vcu.edu)
Date: Fri Mar 04 2011 - 15:07:42 CST

Dear all,
this is the first time I use Namd to run a MD simulation and I need to
equilibrate a simple SPC/E water sample at 300K and 1atm with SHAKE. I
started from a lattice of water molecules with SPC/E geometry at very low
density in order to avoid superimpositions. The PBC cell is correctly
centered and sized and the simulation ran without evidence of
superimpositions. As you can see from the input script below I ran an NPT
simulation with temperature rescaling and langevin barostat. However the
calculated pressure never reached the desired value, with strong
oscillations (hundreds atm) around zero, and the compression stopped at
densities higher than that expected for water.
What is wrong?

numsteps 100000
timestep 1
firsttimestep 0
stepspercycle 20

nonbondedFreq 1
fullElectFrequency 1

cutoff 10
switching off
switchdist 8
pairlistdist 12

exclude scaled1-4
1-4scaling 1

rigidBonds all
rigidTolerance 0.00000001
rigidIterations 100
rigidDieOnError on

vdwGeometricSigma yes

PME on
PMETolerance 0.00001
PMEInterpOrder 4
PMEGridSpacing 1

dielectric 1

ZeroMomentum yes

cellBasisVector1 68 0 0
cellBasisVector2 0 68 0
cellBasisVector3 0 0 68
cellOrigin 34 34 34

wrapAll off

temperature 300
COMmotion no

rescaleTemp 300
rescalefreq 5

langevinPiston on
langevinPistonTarget 1.01325
langevinPistonTemp 300
langevinPistonDecay 200
langevinPistonPeriod 400

useFlexibleCell no
useGroupPressure yes

coordinates water_5K.pdb
structure water_5K.psf
paratypeCharmm on
parameters spce_water.par

outputEnergies 50

binaryoutput no
outputname water_r1

binaryrestart yes
restartname water_r1_rst
restartfreq 10000

DCDfile water_r1.dcd
DCDfreq 1000

XSTfile water_r1.xst
XSTfreq 1000

This is my parameter file for SPC/E water

BONDS
OSP HSP 450.000 1.0000
HSP HSP 0.000 1.6330

ANGLES
HSP OSP HSP 55.000 109.4700

NONBOND
HSP 0.000000 -0.000001 0.000000
OSP 0.000000 -0.155350 1.582760

END

whether the topology file is

18 1

MASS 1 HSP 1.00797 H
MASS 2 OSP 15.99940 O

DEFAULT FIRST NONE LAST NONE

RESI SPE 0.0000
GROUP
ATOM O OSP -0.8476
ATOM HA HSP 0.4238
ATOM HB HSP 0.4238
BOND O HA O HB HA HB
ANGLE HA O HB
DONOR HA O
DONOR HB O
ACCEPTOR O
PATCHING FIRST NONE LAST NONE
END

Thank you to anyone could help me.

Davide

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