[gmx-users] problem regarding cut-off and the PME grid spacing

Mark Abraham mark.j.abraham at gmail.com
Wed Apr 20 10:51:14 CEST 2016


The information message and the actual error are separated in your log file
with a bunch of punctuation because they're logically separate.

Anyway, there should also have been a link to
http://www.gromacs.org/Documentation/Errors which suggests some strategies
for this issue.


On Wed, 20 Apr 2016 09:00 Tuhin Samanta <samantatuhin1991 at gmail.com> wrote:

> Hello ,
> My system involves water molecules in a box of 5x5x5 nm3. When I was doing
> the simulation for energy minimization I  got n error message --
> The optimal PME mesh load for parallel simulations is below 0.5
>   and for highly parallel simulations between 0.25 and 0.33,
>   for higher performance, increase the cut-off and the PME grid spacing
>  4 particles communicated to PME node 4 are more than 2/3 times the cut-off
> out of the domain decomposition cell of their charge group in dimension x.
> This usually means that your system is not well equilibrated.
> I have changed the cut off and grid spacing but still it's showing the
> error message. I know it is the problem with the parallelization. Also I
> have  gone through the user forum's discussion.  So can anyone please
> suggest me how to get rid of that problem.
> Thank you so much.
> Best regards,
> Tuhin
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