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

Ramon Guixà ramonguixxa at gmail.com
Wed Oct 31 23:57:46 CET 2018

Hi Chris,
I actually use the mdp file suggested by CHARMM-GUI. I figured they had
tested this set-up extensively.
Regarding the wacky init pdb, it has indeed been previously equilibrated
using the Berendsen barostat for 20 ns, however, I will now run, as you
suggest, a much longer equilibration step before switching to the
Parrinello-Rahman production run, just to see if the init file gets better.
Thanks a lot for the feedback!

On Wed, Oct 31, 2018 at 5:40 PM Chris Neale <candrewn at gmail.com> 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.
> Thank you,
> Chris.
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