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

[Mark Abraham]

That's just the first stage of an equilibration. See
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
for suggestions

Mark

On Wed, 20 Apr 2016 19:20 Tuhin Samanta <samantatuhin1991 at gmail.com> wrote:

> I have done the energy minimization many times by taking previously
> minimized structure.
>
>
>
> On Wed, Apr 20, 2016 at 10:39 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > On Wed, 20 Apr 2016 19:04 Tuhin Samanta <samantatuhin1991 at gmail.com>
> > wrote:
> >
> > > 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.
> > >
> >
> > Then what did you change? You may need to be more gentle.
> >
> > Secondly by changing rcut and PME mesh girding I have tried a lot. But
> it's
> > > showing same error message.
> > >
> >
> > Those suggestions are made for perhaps improving performance, which is
> > unrelated to your error. They just both happen to use the word PME...
> >
> > So can you please tell me any specific solution for this problem.
> > >
> >
> > They're all at
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up
> >
> > Mark
> >
> > 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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