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

Justin A. Lemkul jalemkul at vt.edu
Mon Jun 15 13:59:16 CEST 2009

Anirban Ghosh wrote:
> Hi ALL,
> 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.

I recently updated the site with some suggestions for such temperatures.  There 
is no substitute, however, for reading the literature (both experimental and 
theoretical) to understand what others are doing and why they are doing it.


> Regards,
> *Anirban Ghosh*
> *Grade Based Engineer
> Bioinformatics Team
> Centre for Development of Advanced Computing (C-DAC)
> Pune, India
> *
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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