[gmx-users] Re: Re: Energy conservation of rigid water models

[Janne Hirvi]

> Have you compiled gromacs in single precision?
> I think double precision compilation is critical
> for energy conservation in NVE.

Yes, I have used only single precision compilation because it has been enough
accurate until now (NPT/NVT). Actually I just want to know if employed time
step of 2fs is applicable and so I think that I should use same compilation
also for energy conservation simulation in NVE ensemble. Or may I prove
suitability of this long time step with double precision compilation even I
have done other simulations with single precision compilation?

Janne


> 2006/2/16, Janne Hirvi <janne.hirvi at joensuu.fi>:
> >
> > Hello!
> >
> > I have read several messages about energy conservation problems and
> > solutions
> > but however I am not sure if I have done something stupid. I have used
> > time
> > step of 2.0fs for rigid SPC and SPC/E water models in simulations of bulk
> > water
> > (NPT) and water droplets on frozen polymer surfaces (NVT). Everything
> > seemed to
> > be just fine but when I tested energy conservation of bulk model in NVE
> > ensemble I was terrified.
> >
> > NVE bulk simulation of 1372 rigid SPC water molecules with 2fs time step
> > (total
> > time 500ps) resulted in huge drift in total energy. I used same parameters
> > as
> > for other simulations and even those aren't optimal I expected atleast
> > something better. Energy conservation seemed to be adequate only when I
> > used as
> > short time step as 0.5fs.
> >
> >
> > Time step (fs)      Total Energy (kJ/mol)      Drift
> >
> > 2.0                 -45596.6                   1235.5
> > 1.0                 -46147.5                   330.974
> > 0.5                 -46331.1                   <10 (not yet finished)
> >
> >
> > Parameters:
> >
> > comm-mode                = None or Linear
> > nstlist                  = 5 or 10
> > rlist                    = 1.2
> > coulombtype              = PME
> > rcoulomb                 = 1.2
> > vdw-type                 = Cut-off
> > rvdw                     = 1.2
> > fourierspacing           = 0.12
> > pme_order                = 4
> > ewald_rtol               = 1e-05
> > ewald_geometry           = 3d
> > tcoupl                   = No
> > Pcoupl                   = No
> >
> >
> > Bad energy conservation indicates that employed time step of 2.0fs is too
> > long
> > but however other results from NPT bulk simulations are reasonable.
> > Moreover I
> > think that its quite normal to use this long time step for rigid water
> > molecules. So I am willing to know if this large energy conservation
> > problems
> > are acceptable and are they atleast "partially compensated" in NPT or NVT
> > ensemble when temperature coupling prevents heating of the system?
> >
> >
> >
> > Thanks for any help or comments!
> >
> > Janne
> >
> >
> >
>
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> > Janne Hirvi, MSc(Physical Chemistry), Researcher
> > University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu,
> > FI
> > Tel: +358 13 2514544 & +358 50 3474223
> > E-mail: Janne.Hirvi at joensuu.fi & hirvi at cc.joensuu.fi
> >
> >
>
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