[gmx-users] Possible Bug GROMACS 3.3.1 - NMA

David van der Spoel spoel at xray.bmc.uu.se
Tue Sep 5 16:38:02 CEST 2006

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.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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