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

Chris Neale candrewn at gmail.com
Wed Oct 31 17:40:05 CET 2018

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

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

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.

Thank you,

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