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 > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
