; VARIOUS PREPROCESSING OPTIONS ; Preprocessor information: use cpp syntax. ; e.g.: -I/home/joe/doe -I/home/mary/hoe include = ; e.g.: -DI_Want_Cookies -DMe_Too define = -DPOSRES ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit = 0 dt = 0.004 nsteps = 250000 ; For exact run continuation or redoing part of a run ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 init_step = 0 ; mode for center of mass motion removal ; comm_mode = Angular comm_mode = Linear ;comm_mode = None ; number of steps for center of mass motion removal nstcomm = 500 ; group(s) for center of mass motion removal comm_grps = System ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd_fric = 0 ld_seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol = 10 emstep = 0.01 ; Max number of iterations in relax_shells niter = 20 ; Step size (ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr = 10 ; TEST PARTICLE INSERTION OPTIONS rtpi = 0.05 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 100 nstvout = 100 nstfout = 0 ;; Output frequency for energies to log file and energy file nstlog = 100 nstenergy = 1 ;; Output frequency and precision for xtc file nstxtcout = 100 xtc_precision = 1000 ; 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 = 5 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no ; nblist cut-off rlist = 1.50 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME ;rcoulomb_switch = 1.1 rcoulomb = 1.5 ; Relative dielectric constant for the medium and the reaction field epsilon_r = 1 epsilon_rf = 1 ; Method for doing Van der Waals vdwtype = SHIFT ; cut-off lengths rvdw_switch = 1.1 rvdw = 1.3 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = no ; Extension of the potential lookup tables beyond the cut-off table-extension = 0.4 ; Seperate tables between energy group pairs energygrp_table = ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; 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 = 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = yes ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = No ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 2 ; Dielectric coefficient of the implicit solvent gb_epsilon_solvent = 80 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; Scaling factors used in the OBC GB model. Default values are OBC(II) gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA ; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2. sa_surface_tension = 2.092 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = Nose-Hoover ; Groups to couple separately tc_grps = System ; Time constant (ps) and reference temperature (K) tau_t = 0.5 ref_t = 298 ; Pressure coupling Pcoupl = no Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p = 1 compressibility = ref_p = ; Scaling of reference coordinates, No, All or COM refcoord_scaling = No ; Random seed for Andersen thermostat andersen_seed = 815131 ; OPTIONS FOR QMMM calculations QMMM = no ; Groups treated Quantum Mechanically QMMM-grps = ; QM method QMmethod = ; QMMM scheme QMMMscheme = normal ; QM basisset QMbasis = ; QM charge QMcharge = ; QM multiplicity QMmult = ; Surface Hopping SH = ; CAS space options CASorbitals = CASelectrons = SAon = SAoff = SAsteps = ; Scale factor for MM charges MMChargeScaleFactor = 1 ; Optimization of QM subsystem bOPT = bTS = ; SIMULATED ANNEALING ; Type of annealing for each temperature group (no/single/periodic) annealing = no ; Number of time points to use for specifying annealing in each group annealing_npoints = ; List of times at the annealing points for each group annealing_time = ; Temp. at each annealing point, for each group. annealing_temp = ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = no gen_temp = 298 gen_seed = 173529 ; OPTIONS FOR BONDS constraints = all-bonds ; Type of constraint algorithm constraint_algorithm = LINCS ; Do not constrain the start configuration continuation = no ; Use successive overrelaxation to reduce the number of shake iterations Shake-SOR = no ; Relative tolerance of shake shake_tol = 0.0001 ; Highest order in the expansion of the constraint coupling matrix lincs_order = 6 ; Number of iterations in the final step of LINCS. 1 is fine for ; normal simulations, but use 2 to conserve energy in NVE runs. ; For energy minimization with constraints it should be 4 to 8. lincs_iter = 2 ; Lincs will write a warning to the stderr if in one step a bond ; rotates over more degrees than lincs_warnangle = 30 ; Convert harmonic bonds to morse potentials morse = no ; ENERGY GROUP EXCLUSIONS ; Pairs of energy groups for which all non-bonded interactions are excluded energygrp_excl = ; WALLS ; Number of walls, type, atom types, densities and box-z scale factor for Ewald nwall = 0 wall_type = 9-3 wall_r_linpot = -1 wall_atomtype = wall_density = wall_ewald_zfac = 3 ; COM PULLING ; Pull type: no, umbrella, constraint or constant_force pull = umbrella pull_geometry = distance pull_dim = Y N N pull_start = yes pull_ngroups = 1 pull_group0 = Na+ pull_group1 = I- pull_vec1 = 1 0 0 pull_rate1 = 0.00 pull_k1 = 5000 ; NMR refinement stuff ; Distance restraints type: No, Simple or Ensemble disre = No ; Force weighting of pairs in one distance restraint: Conservative or Equal disre-weighting = Conservative ; Use sqrt of the time averaged times the instantaneous violation disre-mixed = no disre-fc = 1000 disre-tau = 0 ; Output frequency for pair distances to energy file nstdisreout = 100 ; Orientation restraints: No or Yes orire = no ; Orientation restraints force constant and tau for time averaging orire-fc = 0 orire-tau = 0 orire-fitgrp = ; Output frequency for trace(SD) and S to energy file nstorireout = 100 ; Dihedral angle restraints: No or Yes dihre = No dihre-fc = 1000 ; Free energy control stuff free_energy = no init_lambda = 0 delta_lambda = 0 sc_alpha = 0 sc_power = 0 sc_sigma = 0.3 couple_moltype = couple_lambda0 = vdw-q couple_lambda1 = vdw-q couple_intramol = no ; Non-equilibrium MD stuff acc_grps = accelerate = freezegrps = freezedim = cos_acceleration = 0 deform = ; Electric fields ; Format is number of terms (int) and for all terms an amplitude (real) ; and a phase angle (real) E_x = E_xt = E_y = E_yt = E_z = E_zt = ; User defined thingies user1-grps = user2-grps = userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0