[gmx-users] Re: genion

Ewaru edina_wang at yahoo.com
Fri May 3 17:52:58 CEST 2013

Hi Justin,

Thank you for your prompt reply! My grompp goes like this: "grompp -f
minim.mdp -c m4_solv_ions.gro -p topol.top -o em.tpr"

Is it in the topol.top file? The reason I'm asking this is because I
obtained this error while running MD: 

"Fatal error:
2 particles communicated to PME node 2 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"

and thus I was checking if my ions are neutralised or not. 

Thanking you in advance.

Best regards

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