On Thu, Jun 13, 2013 at 11:59 PM, Parker de Waal <parker.dewaa...@kzoo.edu>wrote:
> 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 > This is normal, see http://www.gromacs.org/Documentation/Terminology/Pressure > > 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 Seems fine, apart from fourierspacing being rather more lax than normal. Be sure your settings are compatible with those used for your force field. Mark > > > 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 > -- 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
