[gmx-users] Water models and diffusion coefficient

David van der Spoel spoel at xray.bmc.uu.se
Sat Feb 9 14:45:23 CET 2013

On 2013-02-09 14:21, Joinforfun Doe wrote:
> Hello,
> I am simulating a model of heavy water, with charges modified from SPCE
> model. This was proposed by Grigera [2001], with H replaced by D and
> charges on O and H increased from values proposed in SPCE model.
> I have verified by using gmxdump that gromacs sees the mass of H as 2.014
> amu and the charges as specified in the topology file. The density comes
> out as expected for heavy water. The system equilibrates well (well-defined
> fluctutations, no trends in energy, density, pressure, temperature)
> However, the diffusion coefficient is always lower than that expected for
> the model. By using the same parameter files I ran a simulation for normal
> water (SPCE) model and the diffusion coefficient matches with that reported
> from other simulations.
> Is there something else that I should check? or is there something about
> g_msd that I am missing?
> Any pointers would be really helpful.
> Thanks
Most water models have too high D. (see J Chem Phys 108 pp. 10220-10230 
(1998)). SPC/E is about right. However that is more luck than skill so 
to speak, since there still is a lot of physics missing from this 
extremely simple model. So if you can reproduce literature values for 
the model and some experimental data, dens, DHvap, then this is as good 
as it gets.

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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