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; ; File 'mdout.mdp' was generated ; By user: kangsgo (1000) ; On host: kangsgo-pc ; At date: Thu Dec 31 22:38:07 2015 ; 5.02参数所有备注 ; ; VARIOUS PREPROCESSING OPTIONS ; Preprocessor information: use cpp syntax. ; e.g.: -I/home/joe/doe -I/home/mary/roe include = -I../top ; 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 dt = 0.002 nsteps = 500000 ; 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 = 100 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 = 5000 nstvout = 5000 nstfout = 0 ; Output frequency for energies to log file and energy file nstlog = 5000 nstcalcenergy = 100 nstenergy = 250 ; Output frequency and precision for .xtc file nstxout-compressed = 250 compressed-x-precision = 1000 ; This selects the subset of atoms for the compressed ; trajectory file. You can select multiple groups. By ; default, all atoms will be written. compressed-x-grps = Protein ; Selection of energy groups energygrps = Protein SOL ; NEIGHBORSEARCHING PARAMETERS ; cut-off scheme (Verlet: particle based cut-offs, group: using charge groups) cutoff-scheme = Verlet ; 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 error due to the Verlet buffer in kJ/mol/ps per atom, ; a value of -1 means: use rlist verlet-buffer-tolerance = 0.005 ; nblist cut-off rlist = 0.8 ; long-range cut-off for switched potentials rlistlong = -1 nstcalclr = -1 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = cut-off coulomb-modifier = Potential-shift-Verlet rcoulomb-switch = 0 rcoulomb = 1.4 ; Relative dielectric constant for the medium and the reaction field epsilon-r = 1 epsilon-rf = 0 ; Method for doing Van der Waals vdw-type = Cut-off vdw-modifier = Potential-shift-Verlet ; cut-off lengths rvdw-switch = 0 rvdw = 0.8 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Separate 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-rtol-lj = 0.001 lj-pme-comb-rule = Geometric ewald-geometry = 3d epsilon-surface = 0 ; 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 print-nose-hoover-chain-variables = no ; Groups to couple separately tc-grps = Protein SOL ; Time constant (ps) and reference temperature (K) tau-t = 0.1 0.1 ref-t = 300 300 ; pressure coupling Pcoupl = Berendsen Pcoupltype = Isotropic nstpcouple = -1 ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau-p = 1.0 compressibility = 4.5e-5 ref-p = 1.0 ; Scaling of reference coordinates, No, All or COM refcoord-scaling = No ; 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 = yes gen-temp = 300 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 = 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 = no ; ENFORCED ROTATION ; Enforced rotation: No or Yes rotation = no ; Group to display and/or manipulate in interactive MD session IMD-group = ; 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) and S to energy file nstorireout = 100 ; Free energy variables free-energy = no couple-moltype = couple-lambda0 = vdw-q couple-lambda1 = vdw-q couple-intramol = no init-lambda = 0 init-lambda-state = -1 delta-lambda = 0 nstdhdl = 50 fep-lambdas = mass-lambdas = coul-lambdas = vdw-lambdas = bonded-lambdas = restraint-lambdas = temperature-lambdas = calc-lambda-neighbors = 1 init-lambda-weights = dhdl-print-energy = no sc-alpha = 0 sc-power = 1 sc-r-power = 6 sc-sigma = 0.3 sc-coul = no separate-dhdl-file = yes dhdl-derivatives = yes dh_hist_size = 0 dh_hist_spacing = 0.1 ; Non-equilibrium MD stuff acc-grps = accelerate = freezegrps = freezedim = cos-acceleration = 0 deform = ; simulated tempering variables simulated-tempering = no simulated-tempering-scaling = geometric sim-temp-low = 300 sim-temp-high = 300 ; 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 = ; Ion/water position swapping for computational electrophysiology setups ; Swap positions along direction: no, X, Y, Z swapcoords = no ; 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