[gmx-users] membrane equilibrium problem.

[Christoph Freudenberger]

nanyu101 wrote:
> Dear gms-users,
>    I have met a problem when I run NPT/NVT for my lipid bilayer.There are many ion channel models and I want to know which model is the most stable in membrane.So I have done following operations.
> 1.I have made a hole in lipid bilayer(POPC/DPPC) and put my ion channels into this hole.Optimize rudely for my ion channel+lipid system.
> 2.Run NPT or NVT 600ps.Run optimization for NPT or NVT results and this energy is needed.
Why did you do that? Doesn't one average the energy of the equil. MD run?

> 3. I have met a problem in this step. If I run NPT or NVT longer, the energy is lower? Why did this happen?
you're still far from equilibrium.

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