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

[Tuhin Samanta]

Thank Mark for your suggestion.

I was trying to resolve the problem --------
" 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."

First of all I have done the energy minimization for long times for proper
equilibriuation.
Secondly by changing rcut and PME mesh girding I have tried a lot. But it's
showing same error message.

So can you please tell me any specific solution for this problem.


Thanking you,
Tuhin


On Wed, Apr 20, 2016 at 2:21 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> 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.
>
> Mark
>
> 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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