Re: System of POPC bilayer

From: Vinit Rege (
Date: Fri Nov 10 2006 - 12:53:06 CST

I have created a membrane using VMD plugin... but I have been told that it
has to be checked if the membrane resembles practical conditions taking into
account surface tension and everything... I am not an expert in this field
(as yet) and have some deadlines by which I wont be able to learneverything
thats required to do so... my aim is to simulate a protein membrane system
and get Diffusion coefficients out of it to verify Saffman Delbruck
equations... thats is why it would be great if I get a membrane thats
matching to practical conditions for sure... thats the reason I am looking
for something that has already been tested for practical validity...

According to your opinion, how much does a membrane created using VMD
resemble to practical ones?

I have the experimental data of what the rate should be... (for
Bacteriorhodopsnin diffusing in POPC bilayer) ... thats another reason why I
wanted to use Dr.Heller's PDBs. since it uses the same combination...!


On 11/10/06, JC Gumbart <> wrote:
> VMD can build POPC bilayers (see the Membrane plugin). Additionally,
> Scott Feller has a few bilayer pdbs on the web: http://
> 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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