[gmx-users] How to choose lipid molecules?

[Jochen Hub]

liang wrote:
> Dear all,
> I am a freshman to membrane protein simulation, and i was wondering
> how to choose lipid molecules for my system.
> As we know, there are lots of lipid molecules: DMPC, DPPC, POPE.....
> but how do people decide that which type of lipid to use? and what
> kinds of criteria should we follow?
Lipids differ in their chain length, chain saturation, head groups size.
There are, e.g., phospholipids, glycolipids. Some are ionic,
zwitter-ionic, or neutral. They differ in the phases they adopt at
whatever temperature, there are wedge-like and cone-like shapted lipids,
etc. There are parameters for some lipids available (including those you
mentioned), and for many there is no topology availabe (yet). Membranes
may include glycerin, ...

I guess you need to think abount the quetion you want to address and
then choose the lipid you want to simulate. An important issue is, or
course, to simulate a lipid membrane which you may compare to experiments.

Cheers,
Jochen


> Thanks so much!
> Liang
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-- 
************************************************
Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
************************************************