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

[Justin Lemkul]

On 10/31/18 12:39 PM, Chris Neale wrote:
> First, your init.pdb is really wacky. You've got a bleb in the membrane.
> That appears to heal rapidly during simulation, but the Z-axis fluctuations
> look pretty large to me. I suspect you're running into a known problem with
> P-R pressure coupling, which is that oscillations can get out of hand if
> your run start far from equilibrium (which yours clearly does). The
> solution is to run for a while first with Berendsen pressure coupling to
> get the system close to equilibrium and then switch over to P-R for
> production.
>
> I suspect that if you do Berendsen for 100 ns then your P-R simulation will
> be stable on the GPUs as well.
>
> I can not answer any question as to why you seem to be having trouble on
> GPUs and not CPUs, and perhaps your simulation has uncovered a bug
> somewhere, but for now I'd suggest that bad inputs can always yield bad
> outputs with some probability.
>
> If you're still searching for the difference, then I'd look at mdrun
> -notunepme, since that would be one actual difference between CPU and GPU
> runs.
>
> Also, you're not using the charmm force field properly with your .mdp file.
> That could be beside the point, but nstlist = 20 with rlist = 1.2 and your
> other setting is not normal, right? Try nstlist = 10. I realize that
> gromacs is going to mess with this during optimization, but I presume that
> it starts with what you give it.

With the Verlet algorithm, nstlist is basically a meaningless setting in 
the .mdp file; mdrun will adjust it to whatever it likes and assigns a 
suitable buffer for the nonbonded interactions. This happens so early in 
the run that it won't affect anything.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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