; VARIOUS PREPROCESSING OPTIONS title = Production Simulation cpp = /lib/cpp ; RUN CONTROL PARAMETERS integrator = md tinit = 0 ; Starting time dt = 0.002 ; 2 femtosecond time step for integration nsteps = 500000 ; Make it 1 ns ; OUTPUT CONTROL OPTIONS nstxout = 1000 ; Writing full precision coordinates every nanosecond nstvout = 5000 ; Writing velocities every nanosecond nstfout = 0 ; Not writing forces nstlog = 200 ; Writing to the log file every step nstenergy = 200 ; Writing out energy information every step nstxtcout = 50 ; Writing coordinates every 5 ps energygrps = Protein Non-Protein nstlist = 5 ns-type = Grid pbc = xyz rlist = 0.9 coulombtype = Reaction-Field rcoulomb = 1.4 epsilon_rf = 78 epsilon_r = 1 vdw-type = Cut-off rvdw = 1.4 ; Temperature coupling Tcoupl = Berendsen tc-grps = Protein Non-Protein ref_t = 400 400 tau_t = 0.1 0.1 annealing = Single single annealing_npoints = 11 11 annealing_time = 0 20 50 80 100 200 300 500 700 800 850 0 20 50 80 100 200 300 500 700 800 850 annealing_temp = 420 450 430 400 380 360 340 330 320 310 300 420 450 430 400 380 360 340 330 320 310 300 Pcoupl = Berendsen Pcoupltype = Isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = no constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = yes lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30