; ions.mdp - used as input into grompp to generate ions.tpr ; Parameters describing what to do, when to stop and what to save define = -DPOSRES -DPOSRES_SDS ; position restrain the peptide and sds integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; 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 = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ; Buffered neighbor searching ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.4 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.4 ; Short-range electrostatic cut-off rvdw = 1.4 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions