[gmx-users] Energy conservation of rigid water models

[milton sonoda]

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


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
>
>
> ------------------------------------------------------------------------------
> 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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