[gmx-users] Water models and diffusion coefficient

Suzen, Mehmet msuzen at gmail.com
Sat Feb 9 17:29:38 CET 2013


For the record there are Water Models using effective pair potentials:
J. Chem. Phys. 114, 6720 (2001)


On 9 February 2013 14:45, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> 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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