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

Berk Hess hess at kth.se
Sat Mar 16 10:07:34 CET 2013


Yes, that is probably the issue.
I forgot to add a check for Buckingham. I will add this to grompp and mdrun.



On 03/16/2013 03:52 AM, Bu Wang wrote:
> 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.
> Thanks,
> Bu
> On Fri, Mar 15, 2013 at 5:48 PM, Mark Abraham 
> <mark.j.abraham at gmail.com <mailto: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><mailto: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><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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