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<div class="moz-cite-prefix">Hi,<br>
<br>
Buckingham is not a high priority, as it is rarely used.<br>
But you can easily edit the cuda kernel and put in the Buckingham
formula.<br>
The main issue would be to pass the parameters, as LJ uses two
paramater,<br>
but Buckingham three.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 03/16/2013 04:21 PM, Bu Wang wrote:<br>
</div>
<blockquote
cite="mid:CAKaoGzsj2DQHf4vJkhEczwG_dSeE=H95iaZWJciHDoZSg6-TYw@mail.gmail.com"
type="cite">
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Berk,<br>
<br>
Thank you for clarifying the issue. Do hope that the support for
Buckingham potentials could be added soon so we can utilize our
GPU cards.<br>
<br>
Regards,<br>
Bu<br>
<br>
<div class="gmail_quote">On Sat, Mar 16, 2013 at 5:07 AM, Berk
Hess <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:hess@kth.se" target="_blank">hess@kth.se</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">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>
<div class="im"><br>
On 03/16/2013 03:52 AM, Bu Wang wrote:<br>
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>
On Fri, Mar 15, 2013 at 5:48 PM, Mark Abraham <<a
moz-do-not-send="true"
href="mailto:mark.j.abraham@gmail.com">mark.j.abraham@gmail.com</a><mailto:<a
moz-do-not-send="true"
href="mailto:mark.j.abraham@gmail.com">mark.j.abraham@gmail.com</a>>>
wrote:<br>
<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>><mailto:<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>><<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="HOEnZb">
<div class="h5"><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>
That does make it sound like it might be a bug. Can you
take your group scheme .tpr and use mdrun -testverlet
successfully?<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>
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>
<br>
Mark<br>
<br>
<br>
<br>
--<br>
Postdoctoral Researcher<br>
Computational Material Science Laboratory<br>
New York State College of Ceramics<br>
Alfred University<br>
Alfred, NY 14802<br>
<br>
<br>
</div>
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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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