; VARIOUS PREPROCESSING OPTIONS title = include = define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit = 0 dt = 0.002 nsteps = 50000 ;100 ps ld_seed = -1 ; For exact run continuation or redoing part of a run init_step = 0 ; mode for center of mass motion removal comm-mode = Linear ; number of steps for center of mass motion removal nstcomm = 1 nstcalcenergy = 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 = 0 ; Step size (1/ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr = 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 0 nstvout = 0 nstfout = 0 ; Checkpointing helps you continue after crashes nstcheckpoint = 1000 ; Output frequency for energies to log file and energy file nstlog = 10000 nstenergy = 100000 ; Output frequency and precision for xtc file nstxtcout = 10000 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 cutoff-scheme = verlet nstlist = 20 ; ns algorithm (simple or grid) ns-type = Grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist = 1.2 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.1 ; 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 = 1.0 rvdw = 1.1 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; 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 = 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 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics) implicit_solvent = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = v-rescale ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau-t = 0.1 ref-t = 298 ; Pressure coupling Pcoupl = Parrinello-Rahman Pcoupltype = Isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau-p = 5 compressibility = 4.6E-5 ref-p = 1 ; Random seed for Andersen thermostat andersen_seed = 815131 ; 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 = 2 ; List of times at the annealing points for each group annealing_time = 0 250 ; Temp. at each annealing point, for each group. annealing_temp = 0 298 ; 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 unconstrained-start = yes ; Use successive overrelaxation to reduce the number of shake iterations Shake-SOR = no ; Relative tolerance of shake shake-tol = 1e-04 ; 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 = ; 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 = Equal ; 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) to energy file nstorireout = 100 ; Dihedral angle restraints: No, Simple or Ensemble dihre = No dihre-fc = 1000 dihre-tau = 0 ; Output frequency for dihedral values to energy file nstdihreout = 100 ; Free energy control stuff free_energy = yes init_lambda = 0 delta_lambda = 0.00002 sc-alpha = 0 sc-sigma = 0.3 refcoord-scaling = all ; Non-equilibrium MD stuff acc-grps = accelerate = freezegrps = freezedim = cos-acceleration = 0 ; 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