Hello,<br><br>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.<br>
<br>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.<br>
<br>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.<br><br>Thank you very much,<br>Bu<br>