[gmx-users] strange bihavior.

David van der Spoel spoel at xray.bmc.uu.se
Thu Feb 6 16:29:15 CET 2003

On Thu, 2003-02-06 at 13:18, Andrey V Golovin wrote:
> Hello gmx-users,
> I did create nice random mixture of lipids, EM was ok Epot=500. But after adding
> the water (by genbox) EM does not work. Fmax=10e+13 in 50 steps :) very nice one.
> Probably answer is very simple, if not i'll provide my *.mdp files.
Could be PBC, a lipid sticking out of the box, while genbox should
realize this. The high energy seems to say atoms too close to each
other. I think mdrun tells you which atom it is, so you can kick that
one out manually.

It's also possible that your lipids have an atom that genbox doesn't
recognize, and hence gives too small radius. Check the output from

> -- 
> Best regards,
>  Andrey                          mailto:golovin at genebee.msu.su
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Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
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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