[gmx-users] problem with g_rmsf

[Adriana Pietropaolo]

I reread the manual, to be sure and -q is the option for an input 
configuration...


> 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?
> 
> Tsjerk
> 
> 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
> > _____________________________________________
> >
> >
> >
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> 
> 
> 
> --
> 
> 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
> 

-- 
_____________________________________________
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 
_____________________________________________