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<div class="moz-cite-prefix">Hi,<br>
<br>
Yes, that is probably the issue.<br>
I forgot to add a check for Buckingham. I will add this to grompp
and mdrun.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 03/16/2013 03:52 AM, Bu Wang wrote:<br>
</div>
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cite="mid:CAKaoGzu80RMYJeTFqKi-1GKtmU3SCyHZ=0ZOqJgUm0+_XD-9gA@mail.gmail.com"
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Hi Mark,<br>
<br>
Thanks for your attention.<br>
<br>
Taking the group scheme .tpr and -testverlet fails in the same
way. I've opened an issue as per your instruction.<br>
<br>
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.<br>
<br>
Thanks,<br>
Bu<br>
<br>
<div class="gmail_quote">On Fri, Mar 15, 2013 at 5:48 PM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:mark.j.abraham@gmail.com" target="_blank">mark.j.abraham@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im"><br>
<br>
On Fri, Mar 15, 2013 at 8:58 PM, Bu Wang <<a
moz-do-not-send="true" href="mailto:bw2@alfred.edu">bw2@alfred.edu</a><mailto:<a
moz-do-not-send="true" href="mailto:bw2@alfred.edu">bw2@alfred.edu</a>>>
wrote:<br>
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>
</div>
Sounds suspicious. Please open an issue at <a
moz-do-not-send="true" href="http://redmine.gromacs.org"
target="_blank">redmine.gromacs.org</a><<a
moz-do-not-send="true" href="http://redmine.gromacs.org"
target="_blank">http://redmine.gromacs.org</a>> with a
description of your simulation, and preferably .mdp and .tpr
files.<br>
<div class="im"><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>
</div>
That does make it sound like it might be a bug. Can you take
your group scheme .tpr and use mdrun -testverlet successfully?<br>
<div class="im"><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>
</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).<br>
<span class="HOEnZb"><font color="#888888"><br>
Mark<br>
</font></span></blockquote>
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<br>
<br clear="all">
<br>
-- <br>
Postdoctoral Researcher<br>
Computational Material Science Laboratory<br>
New York State College of Ceramics<br>
Alfred University<br>
Alfred, NY 14802
<br>
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