Hi Berk,<br><br>It might be rare in biological simulations, but for simulations of inorganic materials, it is very common. I think it is a shame that the scope of GROMACS is limited to biomaterials. Lots of researches in my field could benefit from the GROMACS' efficiency and functionality. And some small improvements would enable that.<br>
<br>Anyway, I guess we will have to invest some effort to figure this out ourselves. To help us get started, do we need cuda programing experiences to modify this part of the code?<br><br>Thanks,<br>Bu<br><br><br><div class="gmail_quote">
On Sat, Mar 16, 2013 at 12:09 PM, Berk Hess <span dir="ltr"><<a 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>
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>
<div><br>
On 03/16/2013 04:21 PM, Bu Wang wrote:<br>
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><div>On Sat, Mar 16, 2013 at 5:07 AM, Berk Hess <<a href="mailto:hess@kth.se" target="_blank">hess@kth.se</a><mailto:<a href="mailto:hess@kth.se" target="_blank">hess@kth.se</a>>> wrote:<br>
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>
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 href="mailto:mark.j.abraham@gmail.com" target="_blank">mark.j.abraham@gmail.com</a><mailto:<a href="mailto:mark.j.abraham@gmail.com" target="_blank">mark.j.abraham@gmail.com</a>><mailto:<a href="mailto:mark.j.abraham@gmail.com" target="_blank">mark.j.abraham@gmail.com</a><mailto:<a href="mailto:mark.j.abraham@gmail.com" target="_blank">mark.j.abraham@gmail.com</a>>>> wrote:<br>
<div><br>
<br>
On Fri, Mar 15, 2013 at 8:58 PM, Bu Wang <<a href="mailto:bw2@alfred.edu" target="_blank">bw2@alfred.edu</a><mailto:<a href="mailto:bw2@alfred.edu" target="_blank">bw2@alfred.edu</a>><mailto:<a href="mailto:bw2@alfred.edu" target="_blank">bw2@alfred.edu</a><mailto:<a href="mailto:bw2@alfred.edu" target="_blank">bw2@alfred.edu</a>>><mailto:<a href="mailto:bw2@alfred.edu" target="_blank">bw2@alfred.edu</a><mailto:<a href="mailto:bw2@alfred.edu" target="_blank">bw2@alfred.edu</a>><mailto:<a href="mailto:bw2@alfred.edu" target="_blank">bw2@alfred.edu</a><mailto:<a href="mailto:bw2@alfred.edu" target="_blank">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 href="http://redmine.gromacs.org" target="_blank">redmine.gromacs.org</a><<a href="http://redmine.gromacs.org" target="_blank">http://redmine.gromacs.org</a>><<a href="http://redmine.gromacs.org" target="_blank">http://redmine.gromacs.org</a>><<a 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><div><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></div></div></blockquote></div>