Hi Justin, Thank you for your prompt reply! My grompp goes like this: "grompp -f minim.mdp -c m4_solv_ions.gro -p topol.top -o em.tpr"
Is it in the topol.top file? The reason I'm asking this is because I obtained this error while running MD: "Fatal error: 2 particles communicated to PME node 2 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors"; and thus I was checking if my ions are neutralised or not. Thanking you in advance. Best regards -- View this message in context: http://gromacs.5086.x6.nabble.com/genion-tp5007916p5007921.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
