No, it requires six, acutally, for aniisotropic coupling. I decided to use semi-isotropic coupling with the xy compressibilities set to 4.5e-15 (it won't accept 0). This should keep the walls parallel to the z axis from moving and accomplish the same thing. Does this sound right?
On Sat, Mar 12, 2011 at 9:24 AM, David van der Spoel <sp...@xray.bmc.uu.se>wrote: > On 2011-03-12 17.17, Denny Frost wrote: > >> Thanks for answering that question about dispersion, that makes sense. >> Also, The values I currently get with NPT are around 58 mN/m, while the >> average values I get for NVT are around 16 mN/m, but with a variance of >> nearly 100% of that value. I'm beginning to see why you only do >> pressure coupling in the z direction, but gromacs 4.5.3 won't let you >> specify tau_p = 0. Any other way to do pressure coupling in just the z >> direction? >> > check manual. > maybe there is only one tau_p value. > >> Denny >> >> On Sat, Mar 12, 2011 at 8:59 AM, Denny Frost <dsfr...@cableone.net >> <mailto:dsfr...@cableone.net>> wrote: >> >> Is that using anisotropic pressure coupling? >> >> >> On Sat, Mar 12, 2011 at 8:55 AM, David van der Spoel >> <sp...@xray.bmc.uu.se <mailto: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> >> <mailto: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> >> <mailto: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> >> <mailto: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> >> <mailto: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> >> <mailto: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> >> <mailto: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> >> <mailto: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 <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 >> >> >> >> > > -- > 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