Re: Problem with SPC/E water simulation

From: Joshua D. Moore (joshuadmoore_at_gmail.com)
Date: Fri Mar 04 2011 - 17:54:20 CST

Are your VDW parameters right? Why does the HSP have an epsilon of
-0.000001? Also the Oxygen sigma seems to be a bit off (actually it should
be 0.5*2^(1/6)*sigma should it not?).

NONBOND
HSP 0.000000 -0.000001 0.000000
OSP 0.000000 -0.155350 1.582760

I get for SPC/E water

NONBOND
HSP 0.000000 0.000000 0.000000
OSP 0.000000 -0.155354 1.7768574

Unless NAMD has changed their file formats?

I also wouldn't expect rescaling the velocities every 5 steps would give you
correct thermodynamics.

There's a water configuration in the VMD solvate plugin directory which is
liquid that could be used, replicated, etc if you don't want to watch water
melt.

On Fri, Mar 4, 2011 at 4:07 PM, Davide Vanzo/FS/VCU <dvanzo_at_vcu.edu> wrote:

> 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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