[gmx-users] Membrane Generating Algorithms and Tools
periole at inka.mssm.edu
Tue Nov 5 23:03:21 CET 2002
on 11/5/02 3:55 PM, Erik Lindahl at lindahl at stanford.edu wrote:
> 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.
I would do number 1) from Erik's. Equilibration of lipid is
quite long so having a part of it already equilibrated is
probably faster, even though it'll have do equilibrate
again in its new environment.
After a rapid look at the link you gave, the method he proposes
seems to be nice and probably works well. There are different
methods, hopefully equivalent at the end.
Physio & biophys Dept.
Mount Sinai Hospital
New York, NY
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