On 2012-02-21 03:41:07PM -0500, Justin A. Lemkul wrote: > > > Andrew DeYoung wrote: > > Hi, > > > > I am interested in doing a membrane-type simulation, in which I have > > all-atom membrane "walls" parallel to xy plane, at z = -z_0 and z = +z_0 > > (where z_0 is a constant). I would like to run an NPT simulation at 1 atm. > > > > > > What type of pressure coupling should I use? Isotropic pressure coupling > > requires only one input value (either compressibility or reference pressure > > ref_p), whereas I think that semiisotropic, anisotropic, and surface-tension > > pressure coupling require specification of both the compressibility and > > ref_p (tensors). > > > > Clearly, I should not use isotropic pressure coupling, because clearly my > > system is not isotropic. However, what if I do not know and cannot find in > > the literature the compressibility of the liquid system that I am placing > > between the membrane "walls"? If I do not know the compressibility very > > accurately or at all, then it seems that I cannot use semiisotropic, > > anisotropic, or surface-tension pressure coupling. > > > > If you have time, I would like to ask an additional question. Now suppose I > > know the compressibility of the liquid between the membrane. Now what > > pressure coupling type should I use; should I use semiisotropic, > > anisotropic, or surface-tension pressure coupling? Both semiisotropic and > > surface-tension look reasonable. In the manual > > (http://manual.gromacs.org/current/online/mdp_opt.html#pc), semiisotropic > > pressure coupling is useful for systems that are isotropic in x and y, but > > different in z (which is the situation I have here). Surface-tension also > > looks like it describes a similar situation, but it requires the > > specification of the surface tension of the liquid, which I do not know. > > > > I am sorry that my questions are quite vague. If you have time, do you have > > any general thoughts? Or can you please recommend any papers that would > > help me understand and choose between the pressure coupling types? > > > > I doubt I can really answer much of this, but isn't the most pressing > consideration the walls themselves? If they're reasonably rigid, the > compressibility of the fluid layer is largely irrelevant, isn't it? Then > again, > if the walls are not rigid, then they become a liability under pressure > coupling > as they may buckle. Seems to me this should be the principal concern. > > -Justin >
Another consideration is that the documentation states when using built-in implicit walls at z=0 and z=zbox to use anistropic pressure coupling with the x/y compressibility set to 0 "otherwise the surface area will change". Maybe start with that and go from there? -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street [email protected] | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- 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
