[gmx-users] Re: problem with g_anaeig

[Bert de Groot]

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.

Bert

____________________________________________________________________________
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
http://www.mpibpc.gwdg.de/abteilungen/071/bgroot
____________________________________________________________________________