[gmx-users] gromacs+CHARMM36+GPUs induces protein-membrane system collapse?

[Ramon Guixà]

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 <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
> 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
>
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