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

Debajyoti Dutta debajyoti_dutta47 at rediffmail.com
Thu Apr 2 20:32:11 CEST 2015

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 

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?

Thank you so much


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