[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"

[Mark Abraham]

On 2/12/2010 4:16 PM, 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.

I doubt the simulation is OK. This error message is one of several that 
can happen when the system is not well-enough conditioned for the MD to 
be stable. See www.gromacs.org/Documentation/Terminology/Blowing_Up. 
Here, you have atoms moving much faster than GROMACS was engineered to 
expect.

You should be confident that a water drop in a vacuum, and your graphite 
surface are both stable on their own before you try the wetting simulation.

>
> For this situation, is there a way of suppressing this error? Or what 
> else can I do?

Work out why it's poorly conditioned.

Mark