[gmx-users] Pressure coupling and membrane-type simulations

Andrew DeYoung adeyoung at andrew.cmu.edu
Tue Feb 21 18:39:44 CET 2012


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?

Thank you very much for your time!

Andrew DeYoung
Carnegie Mellon University

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