[gmx-users] graph edge limit

David spoel at xray.bmc.uu.se
Thu Nov 10 17:39:12 CET 2005

On Fri, 2005-11-11 at 00:17 +0800, Yang Ye wrote:
> Hi, David
> I recently met this error with 3.3 version's mdrun.
> "More than 12 graph edges per atom (atom xxxx)"
Do you have more than 12 bonds for a single atom?

> My system is a 8-atom stable structure, each of them is bonded and these 
> bonds are transformed to SHAKE constraints. The system is 
> over-constrained with 28 bonds. The error applied to almost each one of 
> them. I did not meet this error with a pre-3.3 cvs version. Is there any 
> workaround to lift this limit?
Not that I know of. In addition you should verify that you have any
degrees of freedom left: 8x3 is 24, so your system should have -4
degrees of freedom.
> Thanks.
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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