<br><br><div class="gmail_quote">On Fri, Mar 15, 2013 at 8:58 PM, Bu Wang <span dir="ltr"><<a href="mailto:bw2@alfred.edu" target="_blank">bw2@alfred.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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>
</blockquote><div><br></div><div>Sounds suspicious. Please open an issue at <a href="http://redmine.gromacs.org">redmine.gromacs.org</a> with a description of your simulation, and preferably .mdp and .tpr files.</div><div>
<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">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>
</blockquote><div><br></div><div>That does make it sound like it might be a bug. Can you take your group scheme .tpr and use mdrun -testverlet successfully?</div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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></blockquote><div><br></div><div>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).</div>
<div><br></div><div>Mark</div></div>