Dear gromacs users, I am doing md simulation of cnt + drug + water molecules. The em.mdp file is follows:
integrator = steep nsteps = 50000 emtol = 10 emstep = 0.01 ns_type = grid rlist = 1.0 coulombtype = PME Cutoff-scheme = Verlet vdwtype = Cut-off rcoulomb = 1.0 rvdw = 1.0 constraints = none periodic_molecules = yes --------------------------------------------------- After using ( gmx_mpi grompp -f em_vac.mdp -c complex.gro -p topol.top -o em_vac.tpr), NOTE 1 [file em_vac.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing. ----------------------------------------------------- Are these parameters true? Which changes I should consider in this mdp file to have not this note? Which cut-off is appropriate? Best, Atila -- 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.
