[gmx-users] Pressure coupling and membrane-type simulations
Peter C. Lai
pcl at uab.edu
Tue Feb 21 23:40:20 CET 2012
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.
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
pcl at uab.edu | Birmingham AL 35294-4461
(205) 690-0808 |
More information about the gromacs.org_gmx-users