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
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