| title = NVT equilibration | |
| define = -DPOSRES ; position restrain the protein and ligand | |
| ; Run parameters | |
| integrator = md ; leap-frog integrator | |
| nsteps = 50000 ; 2 * 50000 = 100 ps | |
| dt = 0.002 ; 2 fs | |
| ; Output control | |
| nstenergy = 500 ; save energies every 1.0 ps | |
| nstlog = 500 ; update log file every 1.0 ps | |
| nstxout-compressed = 500 ; save coordinates every 1.0 ps | |
| ; Bond parameters | |
| continuation = no ; first dynamics run | |
| constraint_algorithm = lincs ; holonomic constraints | |
| constraints = h-bonds ; bonds to H are constrained | |
| lincs_iter = 1 ; accuracy of LINCS | |
| lincs_order = 4 ; also related to accuracy | |
| ; Neighbor searching and vdW | |
| cutoff-scheme = Verlet | |
| ns_type = grid ; search neighboring grid cells | |
| nstlist = 20 ; largely irrelevant with Verlet | |
| rlist = 1.2 | |
| vdwtype = cutoff | |
| vdw-modifier = force-switch | |
| rvdw-switch = 1.0 | |
| rvdw = 1.2 ; short-range van der Waals cutoff (in nm) | |
| ; Electrostatics | |
| coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics | |
| rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) | |
| pme_order = 4 ; cubic interpolation | |
| fourierspacing = 0.16 ; grid spacing for FFT | |
| ; Temperature coupling | |
| tcoupl = V-rescale ; modified Berendsen thermostat | |
| tc-grps = Protein Non-Protein ; two coupling groups - more accurate | |
| tau_t = 0.1 0.1 ; time constant, in ps | |
| ref_t = 300 300 ; reference temperature, one for each group, in K | |
| ; Pressure coupling | |
| pcoupl = no ; no pressure coupling in NVT | |
| ; Periodic boundary conditions | |
| pbc = xyz ; 3-D PBC | |
| ; Dispersion correction is not used for proteins with the C36 additive FF | |
| DispCorr = no | |
| ; Velocity generation | |
| gen_vel = yes ; assign velocities from Maxwell distribution | |
| gen_temp = 300 ; temperature for Maxwell distribution | |
| gen_seed = -1 ; generate a random seed | |