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

Justin Lemkul jalemkul at vt.edu
Wed Oct 31 17:46:06 CET 2018

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 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


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