[gmx-users] GROMACS fatal error for PME rank 1 are more than 2/3 times

[Justin Lemkul]

On 4/2/15 1:26 PM, Debajyoti Dutta wrote:
> Hi all,
>
> Since I am new to deal with GROMACS simulation. I am running a protein -ligand complex simulation in my Mac Book pro with specifications
> below.
>
> Processer 2.2 GHz intel core i7
> Memory 8GB 1333 MHz DDR3
>
> when equilibrating the protein ligand system I am getting the following error massage
>
> WARNING: Listed nonbonded interaction between particles 6226 and 6231
> at distance 2.657 which is larger than the table limit 2.431 nm.
>
> This is likely either a 1,4 interaction, or a listed interaction inside
> a smaller molecule you are decoupling during a free energy calculation.
> Since interactions at distances beyond the table cannot be computed,
> they are skipped until they are inside the table limit again. You will
> only see this message once, even if it occurs for several interactions.
>
> IMPORTANT: This should not happen in a stable simulation, so there is
> probably something wrong with your system. Only change the table-extension
> distance in the mdp file if you are really sure that is the reason.
>
> -------------------------------------------------------
> Program gmx, VERSION 5.0.4
> Source code file: ~/gromacs-5.0.4/src/gromacs/mdlib/pme.c, line: 754
>
> Fatal error:
> 7 particles communicated to PME rank 1 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.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
> Before considering other possibilities for this error I want to make sure if it is feasible to work with the above mentioned machine specification
> for protein ligand complex simulation;
>
> and if the specification is well enough to run the protein-ligand simulation in membrane?
>

That system might be pretty large to expect reasonable performance.  The GROMACS 
memory footprint is pretty small, but the overall throughput may not be great. 
Do some benchmarking.

The error is not related to your hardware, it's a case of the system being 
unstable.  Consult http://www.gromacs.org/Documentation/Terminology/Blowing_Up 
or any of the million other messages in the archive with the same error.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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