Re: NPT_NPgammaT_or_NPAT_for_membrane_with_CHARMM_forcefield

From: Himanshu Khandelia (hkhandel_at_memphys.sdu.dk)
Date: Sun Nov 11 2007 - 05:04:33 CST

> I've also mentioned previously my concern about changing ensembles after
> equilibration. Perhaps that is why the volume changes on going from NVT
> to NPT, again to please reviewers. I was just at a CHARMM tutorial
> where we were told to "never simulate using NVT because experiments are
> always at 1 atm". I think changing horses in mid-stream leads to
> problems, but that is my opinion, I guess. I would also guess that the
> constant P piston is what is causing the membrane to compress.

Please read a basic text book on molecular simulation and statistical
mechanics. "never simulate using NVT" means, never use NVT for sampling.
You need to understand the difference between equilibrium sampling and
equilibration.

For a good review on the source of the problems associated with
implementing constant pressure conditions in a lipid bilayer system, refer
to Scott Feller's excellent little review in the book "Methods in Membrane
Lipids".

----------------------------
Himanshu Khandelia, PhD (Chemical Engineering),
Research Assistant Professor (Postdoc),
MEMPHYS, Center for BioMembrane Physics: www.memphys.sdu.dk
University of Southern Denmark (SDU)
Campusvej 55, Odense M 5230, Denmark
Phone: +45 6550 3510, +45 2398 7972
Fax: +45 6550 4048
email: hkhandel_at_memphys.sdu.dk,
hkhandelia_at_gmail.com
WWW: www.memphys.sdu.dk/~hkhandel
-----------------------------

On Sat, 10 Nov 2007, Richard Wood wrote:

>

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