[gmx-users] How to suppress the error "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group"

[Carsten Kutzner]

On Dec 2, 2010, at 6:16 AM, WU Yanbin wrote:

> Dear GMXers,
> 
> I'm running a simulation of water contact angle measurement on top of graphite surface. 
> Initially a water cubic box is placed on two-layer graphite surface with the rest of the box being vacuum. The water droplet is relaxed during the simulation to develop a spherical shape.
> 
> An error of "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group" was encountered.
> And I have read the suggested solutions at the link below
> 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.
> 
> I guess the reason for this error in my case is because of the vacuum such that the water molecules at the boundary of the droplet can move fast. I have check the trajectory and the simulation is OK.
> 
> For this situation, is there a way of suppressing this error? Or what else can I do?
If the system is small enough, you can run it on a single core and
the problem cannot occur. You could also try to use particle decomposition (-pd) instead
of domain decomposition. Or use less domains, i.e. less cores in total or at least
less PP nodes if you use PME/PP splitting. This will at least reduce the probability for the problem to occur.

Carsten


> 
> PS: the GROMACS version I'm using is GROMACS4.5.
> 
> Thank you.
> 
> Best,
> Yanbin
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne