; Run parameters integrator = md nsteps = 500000 ; 1 ns dt = 0.002 ; 2 fs ; Output control nstxtcout = 50000 ; 10 frames nstenergy = 500 ; save energies every 20 ps nstlog = 500 ; update log file every 20 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = h-bonds ; all bonds+anglesl (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching nstlist = 10 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.2 ; Cut-off for making neighbor list (short range forces) cutoffscheme = verlet rcoulomb = 1.2 ; Short-range electrostatic cut-off vdwtype = cutoff rvdw = 1.2 ; Short-range Van der Waals cut-off ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Periodic boundary conditions pbc = xyz ; Periodic Boundary Conditions (yes/no) ; Temperature coupling is on tcoupl = berendsen ; modified Berendsen thermostat tc-grps = system ; two coupling groups - more accurate tau_t = 1.0 ; time constant, in ps ref_t = 305 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = no ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, in bar compressibility = 4.5e-5 4.5e-5 ;isothermal compressibility of water, bar^-1 ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 305 gen-seed = 100000 ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 10 comm-mode = Linear comm-grps = ; Scale COM of reference coordinates refcoord_scaling = com