[gmx-users] 1 particles communicated to PME rank 3 are more than 2/3 times the cut-off out

[Justin Lemkul]

On 4/1/20 12:04 AM, Seketoulie Keretsu wrote:
> Dear Gromacs Community,
>
> I have come across this problem during NVT equilibration of an all atom
> protein-ligand MD simulation.
>
> Fatal error:
> 1 particles communicated to PME rank 3 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 basically used the nvt and npt equilibration approach given in tutorial
> by Justin. I have tried changing the equilibration process  by gradually
> increasing temperature to 100K. However it still shows the same error. I
> have tried with other conformation of ligand as initial structure also but
> no improvement. Could you advise how to go about this?

http://manual.gromacs.org/current/user-guide/terminology.html#diagnosing-an-unstable-system

Protein-ligand complexes are addressed specifically there. Make sure 
your ligand topology is sufficiently accurate.

-Justin

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Justin A. Lemkul, Ph.D.
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