[gmx-users] Membrane Generating Algorithms and Tools
lindahl at stanford.edu
Tue Nov 5 21:55:35 CET 2002
Tivadar Orban wrote:
> I would like to build a lipid bilayer (POPC/POPS=4:1).
> Did somebody used the algorithm provided by Ilya Balabin at the site:
> 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
I would either
1) Start with a pure POPC bilayer and replace 1 in 4 lipids.
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.
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