[gmx-users] gromacs+CHARMM36+GPUs induces protein-membrane system collapse?
ramonguixxa at gmail.com
Wed Oct 31 16:07:00 CET 2018
Ok, I mean, It makes sense what you say.
I still I don't understand though how this has not been spotted before, I
mean, I presume this combination is widely used (CHARMM+GROMACS+GPUs) and I
have replicated the problem using versions 5, 2016, and 2018...? I know I
sound a little desperate, but is there any workaround I could use to
proceed until this is resolved?
On Wed, Oct 31, 2018 at 3:51 PM Justin Lemkul <jalemkul at vt.edu> wrote:
> On 10/31/18 10:47 AM, Ramon Guixà wrote:
> > Hi Justin,
> > I do not have access to GPUs with ECC, but I have actually run the same
> > in different machines with different GPUs, including GTX 980, 1060 and
> > 1080. In all cases, I get the same problem. Although they are all
> > cards, it is quite unlikely that a bit flip is behind this, isn't it?
> Certainly is. It wasn't clear if you were just running over and over
> again on the same card or what.
> > In fact, I had simulated before CHARMM-GUI systems using GTX cards and
> > never had a problem. Since this has only benn happening recently to me,
> > I am wondering if I should blame the new force field (CHARMM36m) or
> > CHARMM-GUI changed something in the way they generate gromacs topologies?
> I sincerely doubt it's the force field. We validate that extensively
> across many compounds to verify that GROMACS and CHARMM compute the
> forces the same (I do this myself when we produce a new force field
> port). We don't (can't) do that easily on GPU, but if the forces are
> different, that points to a software bug, because everything about the
> CPU implementations is identical. Given that you have a sudden change in
> system behavior, that further points to a software bug, in my opinion,
> because if something was fundamentally wrong with the force field, (1)
> you would see it on CPU runs and (2) it would almost certainly occur
> much earlier in the simulation.
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
> jalemkul at vt.edu | (540) 231-3129
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users