[gmx-users] Re: genion

[Justin Lemkul]

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

-- 
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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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