; Run parameters integrator = md ; leap-frog integrator nsteps = 15000 ; = 30 ps dt = 0.002 ; 2 fs ; Output control nstxout = 50000 ; save coordinates every 1.0 ps nstvout = 50000 ; save velocities every 1.0 ps nstenergy = 50000 ; save energies every 1.0 ps nstlog = 50000 ; update log file every 1.0 ps ; Bond parameters constraints = h-bonds ; No constraints except for those defined explicitly in the topology continuation = yes ; Restarting after NVT constraint_algorithm = lincs ; holonomic constraints lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Nonbonded settings cutoff-scheme = Verlet ; Buffered neighbor searching ns_type = grid ; search neighboring grid cells nstlist = 20 ; 20 fs, largely irrelevant with Verlet scheme rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) DispCorr = EnerPres ; account for cut-off vdW scheme ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; grid spacing for FFT ; Temperature coupling is on tcoupl = nose-hoover ; nose-hoover thermostat tc-grps = LIG SOL _U1M tau_t = 2 2 2 ref_t = 260 260 260 ; Pressure coupling is on pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 4.0 ref_p = 150 ; 15 MPa compressibility = 4.5e-5 refcoord_scaling = com ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Velocity generation gen_vel = no ; Velocity generation is off