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? Ramon
On Wed, Oct 31, 2018 at 3:51 PM Justin Lemkul <jalem...@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 > tpr > > in different machines with different GPUs, including GTX 980, 1060 and > > 1080. In all cases, I get the same problem. Although they are all > non-ECC > > 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, > so > > I am wondering if I should blame the new force field (CHARMM36m) or > whether > > 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 > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * 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-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * 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-requ...@gromacs.org.