title = MD simulation of Hen Egg White Lysozyme cpp = /lib/cpp include = -I../top define = -DFLEXIBLE integrator = md ;Total simulation time: 1200 ps dt = 0.004 ;time step in picoseconds nsteps = 300000 ;number of steps nstxout = 1000 ;frequency to write coordinates to output trajectory file nstvout = 1000 ;frequency to write velocities to output trajectory file nstlog = 1000 ;frequency to write energies to log file nstenergy = 100 ;frequency to write energies to energy file nstxtcout = 1000 ;frequency to write coordinates to xtc trajectory xtc_grps = ;group(s) to write to xtc trajectory energygrps = ;group(s) to write to energy file nstlist = 5 ;Frequency to update the neighbor list (and the long-range forces,when using twin-range cut-off's). ns_type = grid ;Make a grid in the box and only check atoms in neighboring grid cells rlist = 0.9 ;cut-off distance for the short-range neighbor list coulombtype = PME rcoulomb = 0.9 vdwtype = switch rvdw_switch = 0.5 rvdw = 0.8 ; long range Van der Waals cut-off ;rvdw = 0.9 ;treatment of van der waals interactions fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 pbc = xyz ; Periodic boudary conditions in all the directions ;Temperature coupling tcoupl = berendsen tc-grps = SOL DNA tau_t = 0.1 0.1 ref_t = 300 300 ;Simulated Annealing ;annealing = single single ;annealing_npoints = 3 3 ;annealing_time = 0 1 4 0 1 4 ;annealing_temp = 300 300 300 300 300 300 ;Velocity generation gen_vel = yes gen_temp = 300 gen_seed = 173529 ;Constrain all bonds constraints = all-bonds