[gmx-users] g_rmsf -res

[Erik Marklund]

Hi,

yes it can be done with g_covar, but such an average structure is often 
of little physical significace. Imagine for instance the acerage 
structure of a rotating methyle group (it's a bunch of atoms on a line).

Erik

Carla Jamous skrev:
> 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 
> <mailto:tsjerkw at gmail.com>> wrote:
>
>     Hi Carla,
>
>     On Thu, Jun 10, 2010 at 12:03 PM, Carla Jamous
>     <carlajamous at gmail.com <mailto: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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>


-- 
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/