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

nanyu101 nanyu101 at sina.com
Sat Jul 19 04:26:02 CEST 2003

Dear gmx-users,
   Thank you for Dr.Christoph Freudenberger prompt reply. Would you please tell me how long I need to equilibrate my system?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?

Thanks for any comments.

Best wishes,
Xianhui Wu


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