[gmx-users] graph edges bug?

[David van der Spoel]

James Rustad wrote:
> Hi List,
> I am running into a "max graph edges exceeded" problem with
> gromacs 3.3.
> I can run my molecule fine with "pbc = no" but when
> I change it to "pbc = xyz" I get
> -------------------------------------------------------------
> Program mdrun_d, VERSION 3.3
> Source code file: mshift.c, line: 95
> 
> Fatal error:
> More than 9 graph edges per atom (atom 16)
> ----------------------------------------------------------------
> 
> Its a rather complex molecule with lots of dummies attached,
> the molecule itself has 7 atoms and 15 constraints are specified,
> so it should be ok.  Again, it runs fine in the gas-phase with pbc=no
> Has anyone else run into this?

Yes, this is a known bug in 3.3.1, see:

http://bugzilla.gromacs.org/show_bug.cgi?id=66

> Thanks
> Jim Rustad
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-- 
David.
________________________________________________________________________
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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