From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Nov 10 2006 - 08:09:19 CST
VMD can build POPC bilayers (see the Membrane plugin). Additionally,
Scott Feller has a few bilayer pdbs on the web: http://
persweb.wabash.edu/facstaff/fellers/
However, it's doubtful that you would observe real protein diffusion
on a nanosecond timescale. Do you have experimental data indicating
what the expected rate might be?
On Nov 8, 2006, at 1:21 PM, Vinit Rege wrote:
> Hello all,
>
> I am looking for a system of POPC bilayer membrane to be used for
> my project. I am an Aerospace Engineer and my project would not
> lead to any publication or a thesis. I would appreciate if someone
> can get me an equilibrated system of POPC bilayer membrane that can
> be used for simulating lateral diffusion of a protein
> (Bacteriorhodopsin) inserted into it. I can create my own system
> but I would not be sure if its chemically / practically resembling
> to actual bilayers since its difficult for me to look into those
> biochemical aspects with such details. My project is to look at MD
> techniques that can be used by engineers to get fluid properties
> such as diffusion and as I said, it would not lead to any direct
> publication. Can somebody help ?
>
> regards,
> Vinit
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