title = OPLS peptide NVT equilibration ; Run parameters integrator = sd ; Langevin thermostat nsteps = 500000 ; 2 * 500000 = 1000 ps dt = 0.002 ; 2 fs comm-mode = Linear ; remove center of mass translational velocity ; Output control frames nstxout = 500 ; save coordinates every 1.0 ps nstvout = 500 ; save velocities every 1.0 ps nstenergy = 500 ; save energies every 1.0 ps nstlog = 500 ; update log file every 1.0 ps ; Bond parameters continuation = no ; first dynamics run constraints = h-bonds ; all bonds converted to constraints ; Neighborsearching cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 50 ; 0.1 ps, largely irrelevant with Verlet, Frequency to update the neighbor list and long range forces rcoulomb = 333.3 ; short-range electrostatic cutoff (in nm) rvdw = 333.3 ; short-range van der Waals cutoff (in nm) rlist = 333.3 ; short-range neighbour list cut-off ; Electrostatics coulombtype = Cut-off ; Treatment of long range electrostatic interactions vdwtype = Cut-off ; Treatment of long range Van der Waals interactions ; Temperature coupling is on, handled by sd integrator tc-grps = system ; two coupling groups - more accurate tau_t = 2.0 ; time constant, in ps ref_t = 300 ; reference temperature, one for each group, in K nsttcouple = 1 ; ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = no ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 300 ; temperature for Maxwell distribution ld-seed = -1 ; random generator for thermal noise for sd gen_seed = -1 ; generate a random seed