# [gmx-users] Re: help me with g_rmsf...

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Oct 5 20:41:38 CEST 2005

```Hi Rodolfo,

With regards to the first question, the difference is that for the RMSF, you
first determine the average position for each particle and then calculate
the deviation from the average for every time frame, summing the square of
the result and dividing by the number of frames. When using -od, instead of
taking the deviation from the average position, the deviation from the
reference position is taken. In that case the deviations will be larger in
general and the result is heavily dependent on the choice of the reference.
For the most useful results, use -o rather than -od.

The difference between g_rms and g_rmsf is basically that with g_rmsf you
average over time, getting atom or residue specific values, whereas with
g_rms you average over atoms, getting time specific values.

Hope it helps,

Tsjerk

On 10/5/05, mekanix <mekanix at aruba.it> wrote:
>
> And the other question is:
> I would like to know if the result that g_rmsf -od gives is the same that
> I
> will get if I use the time average g_rms per residue
> Thank's very much to all
> mekanix writes:
>
> > Hi Tsjerk, thank you for the answer!
> > But my problem is... I can't completely understand
> > this difference... Maybe rms deviation is a sort of mean value
> > and rmsf a sort of standard deviation?
> > Can you explain me in few words the difference?
> > Thank's very much
> > Rodolfo
> >
> >
> > Hi Rodolfo,
> >
> > Reading the help (g_rmsf -h) tells that "with the option -od the root
> mean
> > square deviation with respect to the reference structure is calculated",
> > which is quite different from the root mean square fluctuation of an
> atom
> > around its average position, which is what you get with -o.
> >
> > Cheers,
> >
> > Tsjerk
> >
> > On 10/5/05, mekanix <mekanix at aruba.it <http://aruba.it>> wrote:
> >>
> >> Hi to all gmx users,
> >> I'm a new gromax user and I use it for my thesis.
> >> I have a question for you about the g_rmsf tool...
> >> I can't understand which is the difference between
> >> using the -o and -od options for the outputs file...
> >> I mean... which kind od results are given by the 2 options
> >> and which are the dif
>
> ferences between them?
> >>
> >> Another question is: one of those two results is maybe
> >> the time average of g_rms per residue?
> >>
> >> Thank's to all
> >> Rodolfo.
> >> _______________________________________________
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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
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
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>
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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
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