[gmx-users] topology error?

David van der Spoel spoel at xray.bmc.uu.se
Fri Jan 10 15:40:18 CET 2003

On Fri, 2003-01-10 at 20:49, Ruben Martinez Buey wrote:
> Hi David,
> Thanks a lot for your reply,
> The starting coordinates comes from EM, and they look like OK. If the
> topology is bad, how can I check where is exactly the error?
> Thanks again

check energies after EM, in particular the components. Coulomb should be
negative and LJ usually too (unless you have much water). A source for
error could also be the 1-4 interactions which should be turned of, e.g.
a COOH group the H-O-C-O interaction can sometimes cause problems.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 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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