title = GerAB Production MD ; Run parameters integrator = md ; leap-frog integrator nsteps = 50000000 ; 2 * 50000000 = 100000 ps (100 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 0 ; save coordinates every 2 ps nstvout = 0 ; save velocities every 2 ps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps nstxtcout = 1000 xtc-precision = 1000 ; Bond parameters continuation = no ; Restarting after NPT constraint_algorithm = lincs ; holonomic constraints constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 4 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; 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 ; Temperature coupling is on tcoupl = V-rescale ; More accurate thermostat tc-grps = Protein_POPG_POPE_TMCL ALA1_K_CL_Water ; three coupling groups - more accurate tau_t = 0.5 0.5 ; time constant, in ps ref_t = 298 298 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z tau_p = 5.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, 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 gen_temp = 298 gen_seed = -1 ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 100 comm-mode = Linear comm-grps = Protein_POPG_POPE_TMCL ALA1_K_CL_Water