[gmx-users] g_rmsf -res

[Carla Jamous]

Hi Tsjerk,

thank you for your answer.
Actually, for the initial structure, I took the values of the B factor, and
calculated the mean square displacement per atom. This is what I meant by
saying RMSF of initial structure. Anyway, thanks for the explanation.

But I have another question: I need to take 3 structures and make an average
structure of these 3. Is there a way to do it with gromacs?

Cheers,
Carla


On Thu, Jun 10, 2010 at 12:15 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>wrote:

> 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
> --
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