[gmx-users] Possible Bug GROMACS 3.3.1 - NMA

[David van der Spoel]

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.
________________________________________________________________________
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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