[gmx-users] error during mdrun

[Justin Lemkul]

On 11/29/12 7:49 AM, Shine A wrote:
> Sir,
>
>     I am studying the dynamics of membrane proteins using KALP-15 in DPPC.
> Now doing nvt equilibration.During mdrun (mdrun -deffnm nvt) getting error
> like this
>    Fatal error:
> 6 particles communicated to PME node 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.
> why this error? How can I solve this?
>

http://www.gromacs.org/Documentation/Errors#X_particles_communicated_to_PME_node_Y_are_more_than_a_cell_length_out_of_the_domain_decomposition_cell_of_their_charge_group

The website has troubleshooting tips by following the link above, and the 
mailing list archive has about a million posts on this topic too.  Surely 
something will be of use.

-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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