[gmx-developers] Segmentation fault switching from group to verlet cutoff shceme

Bu Wang bw2 at alfred.edu
Sat Mar 16 03:52:00 CET 2013

Hi Mark,

Thanks for your attention.

Taking the group scheme .tpr and -testverlet fails in the same way. I've
opened an issue as per your instruction.

I just noticed that the manual says the Verlet scheme only works with plain
LJ. We are using Buckingham potentials for non-bonded interactions. Could
this be the issue? Grompp didn't complain though.


On Fri, Mar 15, 2013 at 5:48 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> On Fri, Mar 15, 2013 at 8:58 PM, Bu Wang <bw2 at alfred.edu<mailto:
> bw2 at alfred.edu>> wrote:
> Hello,
> We encountered a problem with the verlet cutoff scheme in GROMACS 4.6.1. A
> simulation that works fine with the group scheme will crash with
> "Segmentation fault: 11" error using the verlet method. GDB shows that it
> happens in pme.c: 415 idxptr[ZZ] = pme->nnz[tiz], but we are not sure how
> to proceed from here.
> Sounds suspicious. Please open an issue at redmine.gromacs.org<
> http://redmine.gromacs.org> with a description of your simulation, and
> preferably .mdp and .tpr files.
> It is possible that our simulation is blowing up, as we can see the
> non-bonded energy becomes absurd in the very first step after switching to
> verlet scheme. However, we don't see how it is possible that the same
> simulation would work with the group scheme. The group scheme gives correct
> energies, and can run to the end without any problem.
> That does make it sound like it might be a bug. Can you take your group
> scheme .tpr and use mdrun -testverlet successfully?
> To further diagnose the problem, we are wondering how we can let GROMACS
> output the neighbor list. We would also greatly appreciate any suggestion
> to resolve the problem.
> The construction of the neighbour lists is different between group and
> Verlet kernels, so there is not much to gain from inspecting them. Knowing
> the combination of algorithms in use is of more interest (so .mdp and any
> mdrun command line options).
> Mark

Postdoctoral Researcher
Computational Material Science Laboratory
New York State College of Ceramics
Alfred University
Alfred, NY 14802
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