Re: NPT_NPgammaT_or_NPAT_for_membrane_with_CHARMM_forcefield

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Nov 09 2007 - 12:05:54 CST

Here is my thinking on the issue. Someone please correct me if I'm
wrong.

The most accurate way is to simulate at NPAT with the appropriate
area per lipid, although, when simulating with a protein, I don't
think it's obvious how to calculate a precise area/lipid. I think
many of us get away with NPT because we are not interested in the
behavior of the membrane anyway, as long as it keeps the protein
"happy"; it may not be worth the trouble to find the optimal area.
This is assuming your area stabilizes though, which sometimes, it may
not (it can shrink a lot in some cases). Then you will certainly
want to use constant area.

On Nov 8, 2007, at 6:00 AM, Karol Kaszuba wrote:

> Hello,
>
> Based on the literature and previous posts I found that CHARMM
> forcefield does not yield the correct
> bilayer geometry in NPT ensemble, however there are many articles
> in which we can find membrane-protein
> simulation in NPT and no one mentions about the problems with
> bilayer structure - so I am little
> confused - can I use the CHARMM forcefield (release c32b1) to
> simulate POPC membrane in NPT or
> do I have to use NPgamma(surface tension)T or NPAT ?
>
> Thank you in advance,
>
> Regards,
>
> Karol
>
>
>

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