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? Denny
On Sat, Mar 12, 2011 at 8:59 AM, Denny Frost <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 > > 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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