1; RUN CONTROL PARAMETERS 2integrator = sd 3; Start time and timestep in ps 4tinit = 0 5dt = 0.004 6nsteps = 250000 7; For exact run continuation or redoing part of a run 8init_step = 0 9; mode for center of mass motion removal 10comm-mode = Linear 11; number of steps for center of mass motion removal 12nstcomm = 1 13; group(s) for center of mass motion removal 14comm-grps = 15 16; OUTPUT CONTROL OPTIONS 17; Output frequency for coords (x), velocities (v) and fo_ces (f) 18nstxout = 0 19nstvout = 0 20nstfout = 0 21; Output frequency for energies to log file and energy file 22nstlog = 100 23nstenergy = 5000 24; Output frequency and precision for xtc file 25nstxout-compressed = 100 26compressed-x-precision = 1000 27; Selection of energy groups 28energygrps = A B 29 30; NEIGHBORSEARCHING PARAMETERS 31; nblist update frequency 32nstlist = 5 33; ns algorithm (simple or grid) 34ns-type = Grid 35; Periodic boundary conditions: xyz, no, xy 36pbc = xyz 37periodic_molecules = no 38; nblist cut-off 39rlist = 1.4 40 41; OPTIONS FOR ELECTROSTATICS AND VDW 42; Method for doing electrostatics 43coulombtype = User 44rcoulomb-switch = 0 45rcoulomb = 1.4 46; Relative dielectric constant for the medium and the reaction field 47epsilon_r = 1 48epsilon_rf = 80 49; Method for doing Van der Waals 50vdw-type = User 51; cut-off lengths 52rvdw-switch = 0 53rvdw = 1.4 54; Apply long range dispersion corrections for Energy and Pressure 55DispCorr = EnerPres 56; Extension of the potential lookup tables beyond the cut-off 57table-extension = 1 58; Seperate tables between energy group pairs 59energygrp_table = A A B B A B 60; Spacing for the PME/PPPM FFT grid 61fourierspacing = 0.12 62; FFT grid size, when a value is 0 fourierspacing will be used 63fourier_nx = 0 64fourier_ny = 0 65fourier_nz = 0 66; EWALD/PME/PPPM parameters 67pme_order = 4 68ewald_rtol = 1e-05 69ewald_geometry = 3d 70epsilon_surface = 0 71 72; IMPLICIT B VENT ALGORITHM 73implicit_solvent = No 74 75; GENERALIZED BORN ELECTROSTATICS 76; Algorithm for calculating Born radii 77gb_algorithm = Still 78; Frequency of calculating the Born radii inside rlist 79nstgbradii = 1 80; Cutoff for Born radii calculation; the contribution from atoms 81; between rlist and rgbradii is updated every nstlist steps 82rgbradii = 2 83; Dielectric coefficient of the implicit solvent 84gb_epsilon_solvent = 80 85; Salt concentration in M for Generalized Born models 86gb_saltconc = 0 87; Scaling factors used in the OBC GB model. Default values are OBC(II) 88gb_obc_alpha = 1 89gb_obc_beta = 0.8 90gb_obc_gamma = 4.85 91; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA 92; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2. 93sa_surface_tension = 2.092 94 95; OPTIONS FOR WEAK COUPLING ALGORITHMS 96; Temperature coupling 97Tcoupl = no 98; Groups to couple separately 99tc-grps = System 100; Time constant (ps) and reference temperature (K) 101tau_t = 0.2 102ref_t = 300 103; Pressure coupling 104Pcoupl = no 105Pcoupltype = isotropic 106; Time constant (ps), compressibility (1/bar) and reference P (bar) 107tau_p = 0.5 108compressibility = 4.5e-5 109ref_p = 1.0 110; Scaling of reference coordinates, No, All or COM 111refcoord_scaling = No 112 113; GENERATE VELOCITIES FOR STARTUP RUN 114gen-vel = no 115 116; OPTIONS FOR BONDS 117constraints = none 118