title = OPLS Lysozyme NPT equilibration ; Run parameters integrator = md ; leap-frog integrator nsteps = 5000 ; 2 * 500000000 = 1000000 ps = 1000 ns = 1us dt = 0.001 ; 2 fs ; Output control nstxout = 1000 nstvout = 1000 nstfout = 1000 nstenergy = 1000 nstlog = 1000 nstxout-compressed = 1000 ; save compressed coordinates compressed-x-grps = System ; save the whole system ; Bond parameters continuation = yes ; Restarting after NPT constraint_algorithm = lincs ; holonomic constraints constraints = h-bonds ; bonds involving H are constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching cutoff-scheme = Verlet ; Buffered neighbor searching ns_type = grid ; search neighboring grid cells nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme rcoulomb = 4.99 ; short-range electrostatic cutoff (in nm) rvdw = 4.99 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ;coulombtype = Cut-off ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Water ; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; Velocity generation is off