[gmx-users] radius of gyration

delara aghaie d_aghaie at yahoo.com
Mon Jun 11 14:40:50 CEST 2012

Dear Justin.
Thanks for your explanation.
In lyzozyme tutorial the radius of gyration has been plooted against simulation time (there 1000 ps).
When I plot the same graph, the horizontal axis is up to 500 (The number of frames for data calculation).
Although, the gyrate.xvg file has gyration data for these 500 frames, how can I tell gnuplot to plot gyration versus simulation time (1000 ps)?


 From: Justin A. Lemkul <jalemkul at vt.edu>
To: delara aghaie <d_aghaie at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Monday, 11 June 2012, 14:46
Subject: Re: [gmx-users] radius of gyration

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

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