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.
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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