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

Bu Wang bw2 at alfred.edu
Fri Mar 15 20:58:50 CET 2013


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.

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.

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.

Thank you very much,
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