Hi Mark, Thanks for your response,
Currently I'm using the gromos53a6 force field because it is compatible with heme cofactor found within P450. I'll look through the literature again to double check my settings for my NvT, NpT and energy minimization steps as well, however any further insight would be greatly appreciated! Parker On Fri, Jun 14, 2013 at 4:13 AM, Mark Abraham <mark.j.abra...@gmail.com>wrote: > 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 > -- 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
