Re: a philosophical question...

From: Jerome Henin (
Date: Mon Feb 19 2007 - 18:09:49 CST

On Monday 19 February 2007 18:16, Richard Wood wrote:
> As far as someone commenting to me, "do you have any philosophical
> questions about MD?", I would say that I do. In fact, I have many. Here
> is one. I have noticed that several (many?) people are working in the
> field of lipid simulations, in the hope of learning something about cell
> membrane behavior. I am wondering if any of these people take into account
> the fact that a cell membrane is not made up of a single type of lipid, but
> generally more than one, and that some of these lipids are unsaturated (to
> assure that the membrane won't freeze). I would like to know how this is
> handled. The membrane building tool of VMD won't allow the building of a
> mixed lipid bilayer. How does one get around this?

By carefully navigating around tricky questions and mined areas. Lipid
bilayers are just very, very difficult systems, be it for experimental or
computational studies (and the two are completely linked). What we are in now
is a kind of middle-age of lipid simulations, if I may paraphrase KS. If we
don't do more simulations of mixed bilayers, it is certainly not because of
the capabilities of such or such VMD plugin, it is because we mostly don't
know how to simulate them properly. Actually, even our models of most
single-component bilayers are pretty unreliable.
That's why most people prefer to ignore lipid-specific problems and just treat
them as "whatever greasy thing my protein is embedded in". I suppose it is
okay most of the time.

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