[gmx-users] graph edges bug?

Berk Hess gmx3 at hotmail.com
Thu May 4 10:37:58 CEST 2006

>From: "James Rustad" <james.rustad at gmail.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] graph edges bug?
>Date: Wed, 3 May 2006 12:17:48 -0700
>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?

Using pbc=full will circumvent the problem.


More information about the gromacs.org_gmx-users mailing list