[gmx-developers] Nr of graph edges per atom and distance restraints

David van der Spoel spoel at xray.bmc.uu.se
Sat Apr 8 13:18:01 CEST 2006

Bert de Groot wrote:
> Hi,
> I just ran into a problem when using distance restraints. mdrun gives up
> with:
> -------------------------------------------------------
> Program mdrun, VERSION 3.3
> Source code file: mshift.c, line: 95
> Fatal error:
> More than 8 graph edges per atom (atom 529)
> -------------------------------------------------------
> Could it be that distance restraints are not properly taken into account
> when determining maxedge?
> 3.2.1 seems not to have this problem.

It also happens in analysis tools. I've played a bit with mshift.c, 
increasing maxedge etc. but then I get inconsistent shifts.
I filed a bugzilla for this, http://bugzilla.gromacs.org/show_bug.cgi?id=66
I also tried making distance restraints have the CHEMBOND property, but 
it doesn't help either.

Erik, you said you changed graph code, but it doesn't show in CVS 
really, apparently Berk has made changes in August last year (mshift.c 
v. 1.44). After that I have changed some debug output.

Any clues?

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://folding.bmc.uu.se

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