Is that using anisotropic pressure coupling? On Sat, Mar 12, 2011 at 8:55 AM, David van der Spoel <sp...@xray.bmc.uu.se>wrote:
> On 2011-03-12 16.45, Denny Frost wrote: > >> I have run NPT simulations using isotropic and semiisotropic coupling >> with the same results. I have never done coupling in just one direction >> though, how do you do this?. I have never used Dispersion corrections. >> It seems to me that this would help, rather than hurt though since, as >> Aldi said, it will make the system closer to experimental values. I >> will give this a try and see what happens. My question still remains - >> why do NPT and NVT simulations give such different values for surface >> tension? >> Denny Frost >> > > You don't give any values so it is hard to judge. > - NVT may have completely wrong pressure > - Dispersion correction assumes a homogeneous system as regards the average > disperson constant per volume, which you probably do not have. E.g. in an > ice/water surface dispersion correction may induce melting. > > The dispersion correction is *not* to bring your system closer to > experiment but rather to correct for the use of a cut-off. > > - Coupling in one direction: specify e.g. > ref-p = 0 0 1 > compressibility = 0 0 4e-5 > tau_p = 0 0 5 > >> >> On Sat, Mar 12, 2011 at 6:40 AM, aldi asmadi <aldi.asm...@gmail.com >> <mailto:aldi.asm...@gmail.com>> wrote: >> >> David, >> >> I have a question that is still related to your reply. If the bulk >> liquid NPT and the interfacial liquid-vapor NVT simulations are >> performed using dispersion corrections to the pressure and energy, >> while the intefacial liquid-liquid NPAT simulation don't use any >> correction, can we say that all results are valid since we don't give >> the same treatment for all systems? >> >> In the NPT and NVT calculations, we apply corrections in order to >> reduce the discrepancy between the calculated and experimental >> properties (say density and surface tension) as small as possible. >> Here we have more confidence that our molecules in systems behave >> accordingly judging from the macroscopic values we obtain. Meanwhile, >> in the NPAT calculation, we don't use such correction meaning that the >> property (say interfacial tension) is expected to deviate more from >> the experimental value? This indicates that the system behaves >> differently in comparison to the same simulation conducted with >> correction? >> >> Many thanks, >> Aldi >> >> >> On Sat, Mar 12, 2011 at 11:44 AM, David van der Spoel >> <sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>> wrote: >> > On 2011-03-12 06.09, Denny Frost wrote: >> >> >> >> I am running MD simulations on Liquid/Liquid interfaces and >> measuring >> >> the interfacial tension between them. I have found that the >> readings in >> >> NVT simulations are close to experimental values, but have a lot of >> >> variation. I run NPT simulations on the exact same system and >> find the >> >> results show very little variation, but the values are far from >> >> experimental results. Does anyone know why this happens? >> >> >> > Please be more specific. How do you do NPT simulations? This may >> influence >> > the result. To get good result I would suggest to do pressure >> coupling only >> > in the normal direction and to turn off dispersion corrections to >> the >> > pressure. >> > >> > -- >> > 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 <mailto:sp...@xray.bmc.uu.se> >> >> http://folding.bmc.uu.se >> > -- >> > gmx-users mailing list gmx-users@gromacs.org >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org>. >> >> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> -- >> gmx-users mailing list gmx-users@gromacs.org >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > > -- > 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 >
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