Re: membrane simulation: pressure control parameters

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Apr 02 2007 - 17:23:05 CDT

I am not well versed in all the pressure control methods but Nose-
Hoover Langevin seems good enough to me.

Your next question is a little more contentious I think. Certainly,
if you use constantArea, you can't apply a surface tension as well
since they are conjugate variables and can't be controlled
independently. Ideally, you would run with constant pressure and
achieve the "correct" area/lipid for your bilayer; however this is
known to not be the case with the charmm forcefield (I don't know
about others). So constant area and constant surface tension are two
ways to correct for this. But then you need to know what the area/
lipid "should" be and you need to be able to set your membrane up
ahead of time to agree with this.

Most of the time, I run in NPT; if I find the bilayer is not behaving
well (i.e. shrinking without stabilizing), I will consider running in
NPzAT (constant area). This also is highly dependent on what you
want to observe/measure in your simulations.

Here are a few papers you should really consider reading (among other
good ones on the subject, I'm sure):

Feller and Pastor. (1999) J. Chem. Phys. 111:1281-1287.

Gullingsrud and Schulten. (2004) Biophys. J. 86:3496-3509.

Marrink and Mark. (2001) J. Phys. Chem. B. 105:6122-6127.

On Apr 2, 2007, at 6:55 AM, Vlad Cojocaru wrote:

> Dear NAMD users,
>
> I am new to membrane simulations and I would like to ask those of
> you with experience in the arrea whether the Nose-Hoover Langevin
> Piston is the method to use for pressure control. If yes, I would
> also like to ask you whether I should set useConstantArea to "yes"
> and I should use SurfaceTension as well ... If Surface Tension is
> recommended, can somebody point me to an appropriate value for a
> POPC bilayer ?
>
> Thanks a lot in advance
>
> vlad
>
>
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