[gmx-users] mdrun error

[David]

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.
________________________________________________________________________
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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