[gmx-users] membrane equilibrium problem again!!!

Christoph Freudenberger christoph.freudenberger at chemie.uni-ulm.de
Sat Jul 19 11:18:01 CEST 2003

nanyu101 wrote:
> Dear gmx-users,
>    Thank you for Dr.Christoph Freudenberger prompt reply. 
Where did you take that from? I haven't finishes my Ph.D. yet.

> Would you please tell me how long I need to equilibrate my system?
At least as long till your energy E0 has converged.

> I have a few ion channel models and I want to find which one is the best stable in lipid bilayer. Can Gromos or OPLS force field differiate it for me? My operation methods are listed as follows.
> 1.I have to make a hole for my ion channels.
> 2.Run NPT or NVT for my ion channel + lipid bilayer system.
> 3.Optimize the NVT or NPT results and this energy E0 was keeped.
> 4.Remove the ion channel of the optimized result. Run energy minimization for this bilayer with a hole with the same optimized conditions.The energy is E1.
> 5. Optimize my ion channel with the same conditions E2 with the same conditions before being put into bilayer. The energy is E2. In the bilayer,the ion channel was constrainted in x y z directions.
>  The stable energy is E0-E1-E2. Can I do it like this?
The basic idea makes sense to me, but I'm concerned about some details,
especially the miniziation step at the end of each simulation.
I'd rather average the energy over the equilibrated system.
Also I'm not sure if it is correct to use the bilayer with the hole
as a reference.
But I don't have experience with that kind of problems
Isn't there any literature about how to treat such systems?

Christoph Freudenberger
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785

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