[gmx-users] questions related to md.mdp
brettliu123 at 163.com
Wed Apr 6 10:38:03 CEST 2016
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?
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