; VARIOUS PREPROCESSING OPTIONS ; Preprocessor information: use cpp syntax. ; e.g.: -I/home/joe/doe -I/home/mary/roe include = ; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit = 0.0 dt = 0.04 nsteps = 25000000 ; For exact run continuation or redoing part of a run init-step = 0 ; Part index is updated automatically on checkpointing (keeps files separate) simulation-part = 1 ; mode for center of mass motion removal comm-mode = Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps = ; 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 = 0 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file nstlog = 10000 nstcalcenergy = 100 nstenergy = 10000 ; 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 = PROTEIN LIPID SOL_ION ; Selection of energy groups energygrps = LIPID SOL_ION PROTEIN1 PROTEIN2 ; NEIGHBORSEARCHING PARAMETERS ; cut-off scheme (group: using charge groups, Verlet: particle based cut-off's) cutoff-scheme = Group ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic-molecules = no ; Allowed energy drift due to the verlet buffer in kJ/mol/ps per atom, ; a value of -1 means: use rlist verlet-buffer-drift = 0.005 ; nblist cut-off rlist = 1.3 ; long-range cut-off for switched potentials rlistlong = -1 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 ; Relative dielectric constant for the medium and the reaction field epsilon_r = 20 epsilon-rf = 0 ; Method for doing Van der Waals vdw_type = Shift ; cut-off lengths rvdw_switch = 0.9 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; 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 = 10 fourier_ny = 10 fourier_nz = 10 ; EWALD/PME/PPPM parameters pme_order = 4 ewald_rtol = 1e-05 ewald-geometry = 3d epsilon_surface = 0 optimize_fft = no ; 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 = 1 ; 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 gb-dielectric-offset = 0.009 sa-algorithm = Ace-approximation ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA ; The value -1 will set default value for Still/HCT/OBC GB-models. sa-surface-tension = -1 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = Berendsen nsttcouple = -1 nh-chain-length = 10 ; Groups to couple separately tc-grps = PROTEIN LIPID SOL_ION ; Time constant (ps) and reference temperature (K) tau_t = 1.0 1.0 1.0 ref_t = 310 310 310 ; pressure coupling Pcoupl = Berendsen Pcoupltype = semiisotropic nstpcouple = -1 ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p = 1.0 1.0 compressibility = 5e-6 5e-6 ref_p = 1.0 1.0 ; 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 = ; 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 = yes gen_temp = 310 gen_seed = 1 ; OPTIONS FOR BONDS constraints = none ; 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 = 4 ; 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 = 1 ; 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, direction, cylinder or position pull_geometry = position ; Select components for the pull vector. default: Y Y Y pull_dim = Y Y N ; Cylinder radius for dynamic reaction force groups (nm) pull_r1 = 1 ; Switch from r1 to r0 in case of dynamic reaction force pull_r0 = 1.5 pull_constr_tol = 1e-06 pull_start = no pull_nstxout = 10 pull_nstfout = 0 ; Number of pull groups pull_ngroups = 1 ; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2) pull_group0 = PROTEIN1PULL pull_weights0 = pull_pbcatom0 = 0 pull_group1 = PROTEIN2PULL pull_weights1 = pull_pbcatom1 = 0 pull_vec1 = 1.0 0.0 0.0 pull_init1 = 4 0.0 0.0 pull_rate1 = 0.0 pull_k1 = 1000 pull_kB1 = 1000 ; ENFORCED ROTATION ; Enforced rotation: No or Yes rotation = yes ; Output frequency for angle, torque and rotation potential energy for the whole group rot_nstrout = 100 ; Output frequency for per-slab data (angles, torques and slab centers) rot_nstsout = 1000 ; Number of rotation groups rot_ngroups = 2 rot_group0 = PROTEIN1PULL rot_type0 = rm2-pf rot_massw0 = no rot_vec0 = 0.0 0.0 1.0 rot_pivot0 = 0.0 0.0 0.0 rot_rate0 = 0 rot_k0 = 1000 rot_slab_dist0 = 1.5 rot_min_gauss0 = 0.001 rot_eps0 = 0.01 rot_fit_method0 = rmsd rot_potfit_nsteps0 = 21 rot_potfit_step0 = 0.25 ; Rotation group name rot_group1 = PROTEIN2PULL ; Rotation potential. Can be iso, iso-pf, pm, pm-pf, rm, rm-pf, rm2, rm2-pf, flex, flex-t, flex2, flex2-t rot_type1 = rm2-pf ; Use mass-weighting of the rotation group positions rot_massw1 = no ; Rotation vector, will get normalized rot_vec1 = 0.0 0.0 1.0 ; Pivot point for the potentials iso, pm, rm, and rm2 (nm) rot_pivot1 = 0.0 0.0 0.0 ; Rotation rate (degree/ps) and force constant (kJ/(mol*nm^2)) rot_rate1 = 0 rot_k1 = 1000 ; Slab distance for flexible axis rotation (nm) rot_slab_dist1 = 1.5 ; Minimum value of Gaussian function for the force to be evaluated (for flex* potentials) rot_min_gauss1 = 0.001 ; Value of additive constant epsilon' (nm^2) for rm2* and flex2* potentials rot_eps1 = 0.01 ; Fitting method to determine angle of rotation group (rmsd, norm, or potential) rot_fit_method1 = rmsd ; For fit type 'potential', nr. of angles around the reference for which the pot. is evaluated rot_potfit_nsteps1 = 21 ; For fit type 'potential', distance in degrees between two consecutive angles rot_potfit_step1 = 0.25 ; NMR refinement stuff ; Distance restraints type: No, Simple or Ensemble disre = simple ; Force weighting of pairs in one distance restraint: Conservative or Equal disre_weighting = Equal ; Use sqrt of the time averaged times the instantaneous violation disre_mixed = no disre_fc = 1000 disre_tau = 50 ; 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 foreign-lambda = sc-alpha = 0 sc-power = 0 sc-sigma = 0.3 nstdhdl = 10 separate-dhdl-file = yes dhdl-derivatives = yes dh-hist-size = 0 dh-hist-spacing = 0.1 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 = ; AdResS parameters adress = no ; User defined thingies user1-grps = user2-grps = userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0