[gmx-users] g_rmsf -res
tsjerkw at gmail.com
Thu Jun 10 12:15:41 CEST 2010
On Thu, Jun 10, 2010 at 12:03 PM, Carla Jamous <carlajamous at gmail.com> wrote:
> Hi Everyone,
> please I have a question concerning g_rmsf.
> I need to compare the RMSF from my initial structure to the RMSF of my
> average structure.
Single structures (initial c.q. average) do not have an RMSF.
> When I did
> g_rmsf -s .tpr -f .xtc -n .ndx -b xx -e yy -o rmsf
> g_rmsf -s .tpr -f .xtc -n .ndx -b xx -e yy -res -o rmsf
This is not what you did. Please copy/paste command lines.
> I got the same result, when choosing C-alpha for root mean square
Sure, when selecting C-alphas, averaging the RMSF per residue
evidently be identical to calculating the RMSF on an atom basis for
> So please can anyone explain how can I get the average per residue over a
> period of time?
Select 'protein' (and use the -res flag).
Tsjerk A. Wassenaar, Ph.D.
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
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