;UCl3 NVT equilibration ; Run parameters integrator = md ; Run MDsim for NVT equilibration nsteps = 50000 ; 0.0001 * 50,000 = 5 ps = 0.05 ns dt = 0.0001 ; 0.1 fs ; Output control nstxout = 1 ; save coordinates every 0.1 ps nstvout = 1 ; save velocities every 1.0 ps nstenergy = 1 ; save energies every 1.0 ps nstlog = 1 ; update log file every 1.0 ps nstcalcenergy = 1 energygrps = UUCLX CUCLX energygrp_table = UUCLX UUCLX CUCLX CUCLX ; Nonbonded settings cutoff-scheme = group ; Buffered neighbor searching ns_type = grid ; search neighboring grid cells nstlist = 1 ; 10 fs vdw-type = user ; Use Madden potential (user-defined) rvdw = 0.8 ; short-range van der Waals cutoff (in nm) rlist = 0.8 ; comment ; Electrostatics (Stock Settings from BV2) coulombtype = pme-user ; Use Madden Potential (user-defined) rcoulomb = 0.8 ; short-range electrostatic cutoff (in nm) ; Temperature coupling is ON (~Stock Settings from BV2) tcoupl = V-rescale ; modified Berendsen thermostat tc_grps = System ; two coupling groups - more accurate tau_t = 0.1 ; 0.1 ; time constant, in ps ref_t = 1000 ; 300 ; reference temperature, one for each group, in K ; Pressure coupling is OFF ;pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D periodic boundary conditions ; Velocity generation continuation = yes ; continuing with coordinates from minimization stored in em.gro ;gen-vel = yes ; assign velocities from Maxwell distribution ;gen-temp = 300 ; temperature for Maxwell distribution ;gen-seed = -1 ; generate a random seed ; Shell MD Options niter = 40 fcstep = 2.0 emtol = 1