On 5/3/13 11:52 AM, Ewaru wrote:
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:
Yes, you should see 12 ions and 12 fewer water molecules than you had before
running genion. If grompp doesn't complain, then your system is neutral. It's
a rather simple check.
"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.
There are a whole host of reasons this could be happening. Neutralization is
not a likely one.
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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