[gmx-users] Re: problem with g_anaeig

Bert de Groot bgroot at gwdg.de
Fri May 16 13:19:00 CEST 2003

Giovanni Chillemi wrote:
> Dear Bert,
> how are you? We met few years ago in Rome. I found a strange behaviour of
> g_anaeig that seems a bug but I'd like you to check this thing.
> I generate the extreme projections of the first eigenvector with the
> command: g_anaeig -s ../average.pdb -f ../topoCA.xtc -extr -first -1
> -nframes 10 -v ../eigenvec.trr
> and then I selected '1 0' to ask for the projection on the first
> eigenvector. This command produce the file extreme.pdb that I'm sending
> you as attachment. If I do the same thing with the command:
> g_anaeig -s ../average.pdb -f ../topoCA.xtc -extr -first 1 -last 10
> -nframes 10 -v ../eigenvec.trr
> I obtain ten files (from extreme1.pdb to extreme10.pdb) with the
> projections from the first to the tenth eigenvectors but the file
> extreme1.pdb is completely different from extreme.pdb generated with the
> previous command!!
> I'm sending you also extreme1.pdb in attachment. Is there anything that I
> didn't understand?

I would also have expected that the two commands yield the same output,
and to check I repeated your analysis, and reproduced the unexpected behavior:

g_anaeig -extr -first 1 -last 1 -v -f all.xtc -e 10 -s xref.gro
g_anaeig -extr -first 1 -last 2 -v -f all.xtc -e 10 -s xref.gro

the first yields extreme.pdb, which differs from extreme1.pdb from the second.

> Another related question. Is the correct (tell me which one) projection
> inside the space visited during the simulation or the projections obtained
> with g_anaeig can be a magnification of the simulated movement along the
> selected eigenvector?

I'm not sure, but I'd say that the extremes should be the true extremes
encountered in the trajectory without magnification.

I forwarded the message to the gromacs users mailinglist. Perhaps somebody
else (Berk?) can comment on this.


Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Theoretical molecular biophysics group
Am Fassberg 11 
37077 Goettingen, Germany

tel: +49-551-2011306, fax: +49-551-2011089

email: bgroot at gwdg.de

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