[gmx-users] Error during mdrun

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Jan 9 12:50:35 CET 2007

Hi Chetana (and Mark et al.),

Note that this can also be the infamous spinning -NH3 error, which has
been reported primarily for lysines previously on this list (tip:
search the archive). To be sure, as Mark stated, more information is
required. Specifically, at what step the crash occurred and which
atoms were involved. This information is given in the *0.log file.
Although the crash will be at the end of the file, the problem may
have gone on for some while and you will have to search for the first
hint of problems (LINCS warning), and check the atoms involved.
If the crash occurs early during your simulation, it is likely a
problem of equilibration/setup.

(Now why am I always lagging behind Mark with my comments?)...

Hope it helps,


On 1/9/07, Mark Abraham <mark.abraham at anu.edu.au> wrote:
> > Dear all,
> > At times during the md run of my peptide, the run crashes and I get the
> > following error displayed -
> >
> > "Wrote pdb files with previous and current coordinates
> > Wrote pdb files with previous and current coordinates
> > MPI process rank 0 (n0, p3089) caught a SIGSEGV.
> > MPI process rank 1 (n0, p3090) caught a SIGSEGV."
> We'll need more information from the output to be sure, but I suspect if
> you look just before this part of the logfile, you'll see LINCS errors,
> indicating you probably haven't minimized or equilibrated well enough.
> Mark
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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