It won't take zero with the berendsen thermostat, but I only wish to do weak coupling for now. Yes, I only specified the two values for semiisotropic. What I'm asking is will this setup only do z-pressure coupling?
On Sat, Mar 12, 2011 at 9:32 AM, David van der Spoel <[email protected]>wrote: > On 2011-03-12 17.28, Denny Frost wrote: > >> 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? >> >> with semiisotropic you need only two values, with anisotropic either 3 or > 6 values. Zero compressibility should work. > >> On Sat, Mar 12, 2011 at 9:24 AM, David van der Spoel >> <[email protected] <mailto:[email protected]>> 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 >> <[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>>> >> wrote: >> >> Is that using anisotropic pressure coupling? >> >> >> On Sat, Mar 12, 2011 at 8:55 AM, David van der Spoel >> <[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>>> >> 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 >> <[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> <mailto:[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>>>> >> >> 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 >> <[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> <mailto:[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>>>> >> >> 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. >> > [email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> <mailto:[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>>> >> >> >> http://folding.bmc.uu.se >> > -- >> > gmx-users mailing list [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> <mailto:[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>>> >> >> >> > 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. 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Read http://www.gromacs.org/Support/Mailing_Lists >> > >> -- >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> <mailto:[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>>> >> >> >> 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 >> [email protected] <mailto: >> [email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>> >> <mailto:[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>>. >> >> 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. >> [email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> http://folding.bmc.uu.se >> -- >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> 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 >> [email protected] <mailto: >> [email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>. >> 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. >> [email protected] <mailto:[email protected]> >> http://folding.bmc.uu.se >> -- >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> 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 [email protected] >> <mailto:[email protected]>. >> 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. > [email protected] http://folding.bmc.uu.se > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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