Re: NPT_NPgammaT_or_NPAT_for_membrane_with_CHARMM_forcefield

From: Himanshu Khandelia (
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

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

Himanshu Khandelia, PhD (Chemical Engineering),
Research Assistant Professor (Postdoc),
MEMPHYS, Center for BioMembrane Physics:
University of Southern Denmark (SDU)
Campusvej 55, Odense M 5230, Denmark
Phone: +45 6550 3510, +45 2398 7972
Fax: +45 6550 4048

On Sat, 10 Nov 2007, Richard Wood wrote:


This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:31 CST