[gmx-users] membrane mimetics

[Anton Feenstra]

John Simms wrote:

> Hi All,
> A question, I want to do alot of short simultions of a membrane protein
> (~10-20 ps each) and want to avoid traditional membrane (mimetics) due to
> the long equilibration time. I have read that a mixed solvent of
> water:methanol:chloroform can be used to mimic the membrane. Has anyone else
> had any experience with this, or can offer any advise (an equilbrated
> box+itp file would be nice :-))

Peter Tieleman's homepage sports some topologies and equilibrated systems.
Normally, one would need to do equilibation only a few times for several
other simulations to branch from - especially when e.g. mdrun_hole is used
to insert the protein in the membrane.

(As a sidenote, what would you expect to learn from such short simulations
on a system with inherently much longer relaxation times?)


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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