Yes, I'm using Cut-off. And the Error is reproducable.
I'll post the bug report.
Regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
David van der Spoel wrote:
Maik Goette wrote:
Hi
I just observed very strange results with my system (around 700 atoms
in vacuum), when doing normal mode analysis. The eigenvalues were all
negative.
I then took an old nma-system from Bert de Groot and did the nma with
3.3.1 on it and observed the same strange results. After that I tried
3.2.1 on that system and the results were quite similar to the ones
Bert got with 3.1.4.
My vacuum-system yields (more or less) correct (not nice) results on
the first look.
Is there something new to obey in 3.3.1 what isn't mentioned in the
manual (3.11 NMA)?
If not, I would think, there's a bug.
Any suggestions?
Regards
Are you using cut-offs? In that case gromacs uses a different algorithm
now, which might cause the problem. Anyway if you have a reproducible
problem please report a bugzilla and upload the necessary files.
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