[gmx-users] mdrun error

David spoel at xray.bmc.uu.se
Sat Oct 2 17:08:42 CEST 2004

On Sat, 2004-10-02 at 16:48, Hector Mrz-Seara Monne wrote:
> > >     
> > OK that looks fine. Have you verified (md.log file) that these settings
> > have been incorporated in the tpr file?
> It seems that every thing is ok
> > Have you tried visualising the trajectory?
> Every thing seems normal if you make a overall view. But after
> checking one by one all the monomers one of them seem to kill
> itself.The main part of the sistem is very rigid with many impropials
> defined along it, benzene-N=N-benzene ( it must be all in a plane). I
> notice when I was trying to parametrice the molecule that if I try to
> keep it complete plane whit impropial then the structure crash in a
> dyanmic, It seems like the molecule enter in a kind of resonance
> effect that finish with unnatural bond legth and angles and the
> crashing of the system. I pass through this problem changing some
> impropials for propials with a loose in the planarity. It seems that
> this fenomenom is crashing my system again. Have you any suggestion?
> Thank you.

Try equilibrating at lower temperature and/or with a shorter time step.
In particular since you describe this resonance thing. Could it be that
your force constants are too high? You should have roughly 20 time steps
in a complete period of the fastest motion.

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://xray.bmc.uu.se/~spoel

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