Hi everyone, I recently tried to perform an 25 ns simulation on 12 nodes and was greeted with this error around 3.2 ns into the run.
'3 particles communicated to PME node 9 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y.' To my knowledge the system has reached equilibrium as shown by energy minimization, nvt and npt runs prior to the md run. The only thing that concerns me is the Pressure average of 1.9 Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Potential -921529 32000 94074.9 -214425 (kJ/mol) Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Temperature 300.033 0.16 1.57434 -0.790469 (K) Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Pressure 1.94649 0.32 91.4545 1.28586 (bar) Density 1012.96 0.037 0.778484 -0.0126246 (kg/m^3) Additionally here is a link to my md.mdp file https://gist.github.com/ParkerdeWaal/d472bac58aa9cebfc23e#file-gistfile1-sh Any input would be greatly appreciated! Parker -- 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
