Hello, For the record there are Water Models using effective pair potentials: J. Chem. Phys. 114, 6720 (2001) http://dx.doi.org/10.1063/1.1356002
Best, -m On 9 February 2013 14:45, David van der Spoel <sp...@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. > sp...@xray.bmc.uu.se http://folding.bmc.uu.se > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
