Dear All, Based on the on-line lysozyme tutorial,
the first several lines I used for my md.mdp was as following, title = OPLS Lysozyme MD ; Run parameters integrator = md ; leap-frog integrator nsteps = 5000000 ; 2 * 5000000 = 10000 ps, 10 ns dt = 0.002 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 2 ps nstvout = 1000 ; save velocities every 2 ps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps My first question is, besides 2 fs for the dt, can I change dt to 20 fs or 200 fs, or 2000 fs for very long production MD? And what will be the difference for the results of production MD between dt=2 fs and dt=2000 fs? My second question is, the intervals for saving coordinates, velocities, energies, log file should be same, or can the intervals different? My third question is, the intervals for saving coordinates, velocities, energies, log file should be an integer times the dt, or have no relationship with dt? Brett -- 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.
