[gmx-users] Possible Bug GROMACS 3.3.1 - NMA

[Maik Goette]

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

-- 
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/