[gmx-users] error says "segnentation fault"

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Nov 14 09:07:30 CET 2006


It is more likely that due to some very large forces mdrun tries to
'move a particle' to some region of the memory it doesn't have access
to. I'd say the system is wrong. You may have overlapping particles or
something alike. Check your system: the topology, the structure, the
box. You did perform all subsequent steps, right:

energy minimization in vacuum
energy minimization in solvent (NVT)
energy minimization in solvent (NPT)
position restraint MD

After that you should be able to run. Did you run through the
tutorials provided?


On 11/14/06, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> nur avneet wrote:
> > Dear All
> >
> > everytime i give the command mdrun...the terminal stops after some steps
> > and says segmentation fault
> Something is catastrophically broken. This would happen if you attempted
> to move a gromacs installation, messed with some system libraries, or
> possibly moved a binary .tpr file between different machines.
> Re-generate a new .tpr file on the same machine you will run mdrun on.
> If you still have this problem, and there's no indication your
> simulation set-up is wrong somehow, you should re-install gromacs properly.
> The fact that you get some steps to work actually suggests you've got a
> problem with how you're doing your simulation. You'd need to describe
> that to get any useful help, however.
> Mark
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Tsjerk A. Wassenaar, Ph.D.
NMR, Utrecht University,
Padualaan 8,
3584 CH Utrecht, the Netherlands
P: +31-30-2539931
F: +31-30-2537623

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