[gmx-users] NPT equilibration fatal error

[Justin Lemkul]

On 10/12/18 8:09 PM, Stephani Macalino wrote:
> Hello,
> I am equilibrating a protein ligand system in a bilayer membrane and I
> receive this error for my 5th equibiration (4th NPT)
>
> Fatal error:
> 5 particles communicated to PME rank 0 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'm a newbie to this and don't completely understand the error.
> Since it says the previous system is not well equilibrated, should I
> increase the steps for equilibration?

http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

-Justin

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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

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