[gmx-users] g_rmsf -res

[Tsjerk Wassenaar]

Hi Carla,

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
>
> or
>
> 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
> calculation.

Sure, when selecting C-alphas, averaging the RMSF per residue
(sum_over_calphas_in_residue/number_of_calphas_in_residue) will
evidently be identical to calculating the RMSF on an atom basis for
each Calpha.

> 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).

Cheers,

Tsjerk


-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands