; VARIOUS PREPROCESSING OPTIONS title = NVT simulation (constant number, volume and temperature) cpp = /lib/cpp ; RUN CONTROL PARAMETERS integrator = md dt = 0.002 nsteps = 1250 ; OUTPUT CONTROL OPTIONS nstxout = 0 ; No output, except for last frame (coordinates) nstvout = 0 ; No output, except for last frame (velocities) nstfout = 0 ; No output, except for last frame (forces) nstlog = 1 ; Write every step to the log nstenergy = 10 ; Write energies at every step nstxtcout = 0 ; Do not write a compressed trajectory energygrps = Protein Non-Protein ; Write energy information separately for these groups ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type = Grid pbc = xyz rlist = 0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = Reaction-Field rcoulomb = 1.4 epsilon_rf = 78 vdw-type = Cut-off rvdw = 1.4 ; Temperature coupling tcoupl = Berendsen tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 ; Pressure coupling pcoupl = no ; OPTIONS FOR BONDS constraints = all-bonds