[gmx-users] radius of gyration

Justin A. Lemkul jalemkul at vt.edu
Mon Jun 11 12:16:40 CEST 2012

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 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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