; LINES STARTING WITH ';' ARE COMMENTS title = Minimization ; Title of run ;define = -DPOSRES ; position restrain the protein and ligand ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 50.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol emstep = 0.001 ; Energy step size nsteps = 50000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 10 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.2 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.2 ; long range electrostatic cut-off vdwtype = cutoff vdw-modifier = force-switch rvdw-switch = 1.0 rvdw = 1.2 ; long range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions DispCorr = no