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

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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