title = Protein-ligand complex NVE equilibration ; Run parameters integrator = md ; leap-frog integrator nsteps = 5000000 ; 2 * 5000000 fs= 10000 ps = 10NS dt = 0.002 ; 2 fs ; mode for center of mass motion removal comm-mode = ANGULAR ; Output control nstxout = 1000 ; save coordinates every 2 ps nstvout = 1000 ; save velocities every 2 ps nstenergy = 1000 ; save energies every 2 ps nstlog = 500 ; update log file every 1 ps energygrps = CRF ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = hbonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 2 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching PARAMETERS vdw-type = Cut-off nstlist = 0 ; 10 fs ns_type = simple ; search neighboring grid cells pbc = no rlist = 0.0 ; short-range neighborlist cutoff (in nm) rlistlong = 0.0 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = cut-off ; Particle Mesh Ewald for long-range electrostatics rcoulomb-switch = 0 rcoulomb = 0.0 ; short-range electrostatic cutoff (in nm) rvdw = 0.0 ; short-range van der Waals cutoff (in nm) rvdw-switch = 0.0 fourierspacing = 0.16 ; grid spacing for FFT epsilon_r = 1 epsilon_rf = 78 ; EWALD/PME/PPPM parameters pme_order = 4 ; cubic interpolation ; Temperature coupling tcoupl = no ; modified Berendsen thermostat ;tc-grps = CRF ; two coupling groups - more accurate ;tau_t = 0.1 ; time constant, in ps ;ref_t = 300 ; reference temperature, one for each group, in K ; Pressure coupling pcoupl = no ; no pressure coupling in NVT ; Dispersion correction ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 300 ; temperature for Maxwell distribution gen_seed = 290389 ; generate a random seed