Dear Users! I am doing simulation of protein and lipids but facing problem in energy minimization as I run: grompp -f minim.mdp -c system_solv_ions.gro -p topol.top -o em.tpr i received Warnings as: WARNING 1 [file ffnonbonded.itp, line 3098]: Overriding LJ-14 parameters.
WARNING 2 [file minim.mdp]: The sum of the two largest charge group radii (8.718670) is larger than rlist (1.300000) I don't understand how to resolve these warnings.. If I ignore them then at next step (mdrun -v -deffnm em) I get fatal error as: Fatal error: There is no domain decomposition for 12 nodes that is compatible with the given box and a minimum cell size of 8.61095 nm Change the number of nodes or mdrun option -rdd If I do energy minimization using any other command as (mdrun -nt 1) then I don't get EM.GRO file in the output.. Please help me to resolve this issue.. Regards Shabana -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
