[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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users