[gmx-users] problem with g_rmsf

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Feb 13 12:17:05 CET 2006

Hi Adriana,

The option -q is for output and has nothing to do with the rmsf calculation.
In the latter case, I'm not sure what you mean with "the results is
different from zero". You would indeed expect the rmsf to be zero in that
case, except for rounding errors. So, what exactly is different from zero
and by which extent?


On 2/13/06, Adriana Pietropaolo <adriana at ms.fci.unibo.it> wrote:
> Hi gromacs users,
> I've posted last friday, but I didn't have an answer about my doubt.
> I've not well understand how g_rmsf makes the least squares respect to a
> reference structure.
> If I make:
> g_rmsf -f a.xtc -s a.tpr -q standard.pdb -od
> where a.tpr is the run file relative to the xtc trajectory,
> I don't know why if I change the standard pdb, with a run
> configuration, the results is the same, I thought that this part of the
> protein is very rigid, but if I make:
> g_rmsf -f a.pdb -s a.tpr -q a.pdb
> where the reference and input configurations are the same and a.pdb is one
> configuration,
> the results is different from zero.
> So I have a doubt that I' m falling in something, or I bad understand
> something....
> Somebody can help me?
> thanks,
> Adriana
> --
> _____________________________________________
> Adriana Pietropaolo,
> PhD student,
> dipartimento di Chimica Fisica ed Inorganica,
> Facolta' di Chimica Industriale
> Universita' di Bologna
> WEB:www2.fci.unibo.it/~adriana
> Tel 051/6446992
> FAX 051/2093690
> _____________________________________________
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060213/f5b3d895/attachment.html>

More information about the gromacs.org_gmx-users mailing list