[gmx-users] graph edge limit
David van der Spoel
spoel at xray.bmc.uu.se
Fri Nov 11 10:24:57 CET 2005
On Fri, 2005-11-11 at 17:07 +0800, Yang Ye wrote:
> David wrote:
> > 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?
You didn't answer this question.
> I noticed that in the md.log
> Max number of graph edges per atom is 8
> Program mdrun_s_mpi, VERSION 3.3
> Source code file: mshift.c, line: 95
> Fatal error:
> More than 12 graph edges per atom (atom 2256)
> Seems a bug in mdrun...
A limitation is something else than a bug.
> > > 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.
> It shows 0 for the DOF of that group in grompp output. So I think that
> it is okay.
No, it means you will have infinite temperature and hence can not do
> > > Thanks.
> > >
> > >
> Yang Ye
> Computational Biology Lab
> School of Biological Sciences
> Nanyang Technological University
> Tel: 6316-2884
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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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