[gmx-users] Possible Bug GROMACS 3.3.1 - NMA

Maik Goette mgoette at mpi-bpc.mpg.de
Wed Sep 6 10:25:01 CEST 2006

Yes, I'm using Cut-off. And the Error is reproducable.
I'll post the bug report.


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.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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