Date: Mon Feb 17 2014 - 10:53:49 CST
Similar developments seem to be happening with AMBER and lipid14.
From: Kenno Vanommeslaeghe [kvanomme_at_rx.umaryland.edu]
Sent: 17 February 2014 16:43
Subject: Re: namd-l: Membrane and NPAT
I can only speak for the CHARMM force field. Until 4 years ago, the CHARMM
lipid force field required NPAT; without it, the membrane would transition
to a gel phase and contract, causing it to become too wide and the
area/lipid too small. This was cured in the CHARMM36 lipid force field;
see the reference below. For CHARMM36, the standard recommendation is to
use NPT (for a number of reasons including the ones you brought up), and
many studies have since been published following this recommendation. In
other words, your information is outdated.
Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph
W. O'Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor
Vorobyov, Alexander D. MacKerell, Jr. and Richard W. Pastor "Update of
the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six
Lipid Types" J. Phys. Chem. B 2010, 114, 7830-7843
Incidentally, for people who have been following the other discussions
I've been involved in on this list, the article nicely illustrates some of
the subtleties we're dealing with in force field design, and why it is
On 02/17/2014 05:49 AM, José Villalaín wrote:
> Dear All,
> I have been looking for a rationale to a question I have but until now I
> have found no clear answer, neither in the list nor in the literature.
> As far as I know, all works simulating the interaction of a protein with
> a membrane are made using the NPAT ensemble, i.e., constant surface
> area. However, wouldn`t be better to use NPT to allow the protein to
> insert into the membrane ?. I suppose that it would be very difficult
> for a protein to insert spontaneously into the membrane if the surface
> lipids can not move completely free in the xy direction because they are
> constrained by the total area they occupy.
> Thanks a lot in advance for your opinions.
> My very best regards,
-- Scanned by iCritical.
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:08 CST