<html><head><meta http-equiv=Content-Type content="text/html; charset=iso-8859-1"><META name="Author" content="Novell GroupWise WebAccess"></head><body style='font-family: Tahoma, sans-serif; font-size: 13px; '>Hello,<br><br>Have you also tried this simulation with a velocity rescaling thermostat in the equilibration period?<br>Could it be that it then would work better?<br><br>Bests,<br><br>Emanuel<br><br>>>> WU Yanbin <wuyb02@gmail.com> 02.12.10 6.16 Uhr >>><br>
Dear GMXers,<br><br>I'm running a simulation of water contact angle measurement on top of graphite surface. <br>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.<br>
<br>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.<br>And I have read the suggested solutions at the link below<br>
<a href="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">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</a>.<br>
<br>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.<br><br>For this situation, is there a way of suppressing this error? Or what else can I do?<br>
<br>PS: the GROMACS version I'm using is GROMACS4.5.<br><br>Thank you.<br><br>Best,<br>Yanbin<br>
</wuyb02@gmail.com></body></html>