[gmx-users] Simulation Temperature for GPCR in POPC bilayer

Anirban Ghosh anirbanz83 at yahoo.co.in
Mon Jun 15 13:54:06 CEST 2009


Thanks a lot for your replies regarding extending water box. I could finally solve the problem by first removing the periodicity from the original POPC pdb files and then properly using editconf with -box option.
In Justin's tutorial on setting up a membrane simulation, the temperature used is 323K (reason is that temperature should be above phase transition temp ) which has been used in many papers as well. My question: is 323K ok for the embedded protein also?Does'nt it affect its stability? And, is 323K applicable for POPC as well?
Any suggestion is welcome. Thanks a lot in advance.


 Anirban GhoshGrade Based Engineer
Bioinformatics Team
Centre for Development of Advanced Computing (C-DAC)
Pune, India

      From Chandigarh to Chennai - find friends all over India. Go to http://in.promos.yahoo.com/groups/citygroups/
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