title = OPLS Lysozyme NVT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 50000 ; 2 * 50000 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 2500 ; save coordinates every 5.0 ps nstvout = 2500 ; save velocities every 5.0 ps nstenergy = 2500 ; save energies every 5.0 ps nstlog = 2500 ; update log file every 5.0 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = h-bonds ; bonds involving H are constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Nonbonded settings cutoff-scheme = Verlet ; Buffered neighbor searching ns_type = grid ; search neighboring grid cells nstlist = 10 ; 20 fs, largely irrelevant with Verlet ; vdW rvdw = 1.2 ; short-range van der Waals cutoff (in nm) rvdw-switch = 1.0 vdw-modifier = force-switch DispCorr = No ; per CHARMM FF convention ; Electrostatics rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; stochastic Bussi thermostat tc-grps = System tau_t = 1.0 ; value of tau (ps) ref_t = 298 ; temperature (K) ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 298 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed