; VARIOUS PREPROCESSING OPTIONS = ; RUN CONTROL PARAMETERS = integrator = md-vv ;integrator = md ; start time and timestep in ps = tinit = 0 dt = 0.002 nsteps = 50000000 ; mode for center of mass motion removal = comm-mode = None ; number of steps for center of mass motion removal = nstcomm = 10 nstcalcenergy = 1 nstpcouple = 1 nsttcouple = 1 ; group(s) for center of mass motion removal = comm-grps = ; ENERGY MINIMIZATION OPTIONS = ; Force tolerance and initial step-size = emtol = 100 emstep = 0.01 ; Max number of iterations in relax_shells = niter = 20 ; Step size (1/ps^2) for minimization of flexible constraints = fcstep = 0 ; Frequency of steepest descents steps when doing CG = nstcgsteep = 1000 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 0 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 1000 nstenergy = 1000 ; Output frequency and precision for xtc file = nstxtcout = 10000 xtc-precision = 10000 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = xtc-grps = ; Selection of energy groups = energygrps = ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or no = pbc = xyz ; nblist cut-off = rlist = 0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = PME rcoulomb-switch = 0 rcoulomb = 0.9 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r = 1 ; Method for doing Van der Waals = vdw-type = Switch ; cut-off lengths = rvdw-switch = 0.8 rvdw = 0.85 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid = fourierspacing = 0.10 ; FFT grid size, when a value is 0 fourierspacing will be used = fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters = pme_order = 6 ewald_rtol = 1e-06 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = Tcoupl = Nose-Hoover ;Tcoupl = Berendsen ; Groups to couple separately = tc-grps = System ; Time constant (ps) and reference temperature (K) = tau_t = 10.0 ;tau_t = 0.2 ref_t = TEMPERATURE ;Pressure coupling = Pcoupl = MTTK ;Pcoupl = berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p = 10.0 ;tau_p = 0.2 compressibility = 4.5e-5 ref_p = 1.01325 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = yes gen_temp = TEMPERATURE gen_seed = GENSEED ; OPTIONS FOR BONDS = constraints = h-bonds ; Type of constraint algorithm = constraint-algorithm = lincs ; Use successive overrelaxation to reduce the number of shake iterations = Shake-SOR = no ; Relative tolerance of shake = shake-tol = 1e-12 ; Highest order in the expansion of the constraint coupling matrix = lincs-order = 4 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs-warnangle = 90 ; Convert harmonic bonds to morse potentials = morse = no ; Free energy control stuff = free-energy = yes ;free-energy = no nstfep = 50 lmc-stats = barker-transition lmc-mc-move = MOVEMC lmc-weights-equil = yes dhdl-print-energy = yes symmetrized-transition-matrix = yes ;nst-transition-matrix = 50000 nst-transition-matrix = 100000 lmc-repeats = MCREPEATS mc-seed = GENSEED init-lambda-state = 0 init-lambda-weights = 0.0 0.32 -0.46 -1.67 -2.83 -3.66 fep-lambdas = 0.0 0.0 0.0 0.0 0.0 0.0 coul-lambdas = 0.0 0.0 0.0 0.0 0.0 0.0 vdw-lambdas = 0.0 0.3 0.6 0.7 0.8 1.0 sc-alpha = 0.5 sc-power = 1 nstdhdl = 100