Re: Simulation of Eukaryotic membrane protein

From: Jerome Henin (
Date: Wed Jan 24 2007 - 09:58:43 CST

Hi Aaron,
Well, a POPC/POPE mixture seems reasonable. I believe it has been done before,
although I can't remember a particular reference right now.
If I were you, I would watch out for the membrane area, though. If you run
NPT, whatever CHARMM lipids you use will give you an underestimated membrane
area, overestimated tail ordering, and in some cases go to the gel phase.
CHARMM people like Scott Feller and Rick Pastor themselves tend to use
constant area, or at least constant surface tension.
The problem with a PC/PE mixture is: what membrane area should one aim for?
That is probably the main reason why most people stick to one-component
You could try to reproduce CD order parameters typically measured in the
liquid phase, it's rather strongly correlated with the area, so it's not a
bad criterion.

On Monday 22 January 2007 00:23, Aaron Oakley wrote:
> Greetings all.
> I would like to simulate a eukaryotic membrane protein in a lipid
> bilayer.
> The cell it is from has mostly PC and PE lipids. Are any NAMD users able
> to recommend a particular membrane composition based on the available
> lipids?
> Thanks,
> Aaron

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