use of charmm27 & NPT ensemble for lipid bilayer simulation

From: Ruchi Sachdeva (ruchi.namd_at_gmail.com)
Date: Fri Jul 11 2008 - 00:26:17 CDT

Dear all,

I am new to lipid bialyer simulations and facing the following problem. I
have equilibrated my system containing a membrane protein embedded in POPC
bilayer using charmm27 & NPT ensemble on a linux cluster. I found that lipid
tails are overlapping with each other & thus bilayer thickness is getting
reduced throughout the simulation.

Then I found a few namd posts
(link1<http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/6863.html>,
link2 <http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/6393.html>)
mentioning that use of charmm27 & NPT does not give correct lipid bilayer
parameters such as area per lipid (by Jensen et al.,
2004<http://www.biophysj.org/cgi/content/abstract/86/6/3556>)
The parameters deviate from the experimental values. Instead one should
initially equilibrate holding the lipid head groups z coordinates in NPT
ensemble. Once area per lipid is set, then use constant area ie. NPzAT
ensemble. Or one can use NPgammaT simulation also.

Despite this report by Jensen et al., I found papers still using charmm27
force field alongwith NPT ensemble, which is not recommended. Moreover,
nothing is mentioned about lipid parameters. Can anyone please shed some
light on this. Am I missing something?

Thanks and Regards

Ruchi

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