[gmx-users] Understanding the output of g_rmsf

[Tsjerk Wassenaar]

Hi Keith,

Reference frame and reference structure are references to the same
reference. It is the structure supplied with -s, and possibly a subset
of the atoms in there, specified by an index group. The RMSF is indeed
the standard deviation of the atomic displacement. That is an atom or
residue based property defined over a certain time, which is recorded
in the file specified with -o. The RMSD (-od [rmsdev.xvg]) is a
structure based property, defined over a range of atoms per time,
which is recorded for each frame in the trajectory. Thso the -o file
is indexed per atom (or per residue with -res) and the -od file is
indexed per time. Hence the differences between the numbers of
entries. That has nothing to do with the reference.

Best,

Tsjerk

On 11/8/06, Keith Ball <kball at catbio.com> wrote:
>
>
>
>
> Hi,
>
>
>
> I have been a bit confused by the g_rmsf output. In the manual, it says that
> "g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard
> deviation) of atomic positions after first fitting to a reference frame."
> But what *is* the reference frame?
>
>
>
> I assume that this output is what goes to the file specified by –o
> (rmsf.xvg, by default).
>
>
>
> The –od option (which goes to rmsdev.xvg by default) is the rms deviation
> "with respect to the reference structure". What reference structure? Is that
> the same as the "reference frame" mentioned above? I notice that the numbers
> in rmsf.svg and rmsdev.xvg are always different, so I assume not.
>
>
>
> Can anyone explain the difference between what goes into the –o file, and
> what goes into the –od file?
>
>
>
> Also, if I start at a specific frame (say, -b 1000, to start 1ns into the
> trajectory), is the conformation nearest t=1ns the reference
> frame/structure?
>
>
>
> Many thanks,
>
>
>
>  Keith
>
> ============================
>  Keith D. Ball, PhD
>  Staff Scientist
>  Catalyst Biosciences
>  290 Utah Ave
>  S. San Francisco, CA 94080
>
>  650-266-8661 (phone)
>  650-871-2475 (fax)
>  kball at catbio.com
>
> http://www.catbio.com
>  ============================
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
post-doc
NMR, Utrecht University,
Padualaan 8,
3584 CH Utrecht, the Netherlands
P: +31-30-2539931
F: +31-30-2537623