On 6/11/12 5:20 AM, delara aghaie wrote:
Dear Gromacs users
I have a question abut radius of gyration in proteins. I want to calculate it
via MD simulation for calcium pump protein. Following the same method as
described in justin lezozyme tutorial, we have dissolved the protein in water.
I want to know that is it wise to study this parameter for this protein out of
membrane and only in the box of water???
In my opinion, that's not appropriate. The structure of a membrane protein can
be highly sensitive to the environment, so any conclusions you reach would be
suspect in the mind of a skeptical reviewer. Why not embed the protein in a
membrane?
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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