[gmx-users] Membrane Generating Algorithms and Tools

[Erik Lindahl]

Tivadar Orban wrote:

> Hi,
> I would like to build a lipid bilayer (POPC/POPS=4:1).
> Did somebody used the algorithm provided by Ilya Balabin at the site:
>
> http://www.ks.uiuc.edu/~ilya/Membranes/
>
> Or you suggest just using a model assembled by a long term MD 
> simulations on a system composed by water and lipid units in the given 
> ratio?

I would either

1) Start with a pure POPC bilayer and replace 1 in 4 lipids.
or
2) Simulate water+lipids from scratch - we've "folded" membranes in 
30-100 ns, and you don't need very long cutoffs just to fold it. Once it is
in a membrane form you can increase the cutoffs and/or use PME.

Cheers,

Erik