1; RUN CONTROL PARAMETERS 2integrator = sd 3; Start time and timestep in ps 4tinit = 0 5dt = 0.002 6nsteps = 100000 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 forces (f) 18nstxout = 200 19nstvout = 0 20nstfout = 200 21; Output frequency for energies to log file and energy file 22nstlog = 0 23nstenergy = 200 24; Output frequency and precision for xtc file 25nstxout-compressed = 200 26compressed-x-precision = 1000 27; Selection of energy groups 28energygrps = LJ1 LJ2 29 30; NEIGHBORSEARCHING PARAMETERS 31; nblist update frequency 32nstlist = 10 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 = 1.2 40 41; OPTIONS FOR ELECTROSTATICS AND VDW 42; Method for doing electrostatics 43coulombtype = Reaction-Field 44rcoulomb-switch = 0 45rcoulomb = 1.2 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 = 1.2 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 = LJ1 LJ1 LJ1 LJ2 LJ2 LJ2 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 SOLVENT ALGORITHM 73implicit_solvent = No 74 75 76; OPTIONS FOR WEAK COUPLING ALGORITHMS 77; Temperature coupling 78Tcoupl = no 79; Groups to couple separately 80tc-grps = System 81; Time constant (ps) and reference temperature (K) 82tau_t = 0.5 83ref_t = 85 84; Pressure coupling 85Pcoupl = No 86;Pcoupl = Parrinello-Rahman 87Pcoupltype = isotropic 88; Time constant (ps), compressibility (1/bar) and reference P (bar) 89tau_p = 0.5 90compressibility = 4.5e-5 91ref_p = 1.0 92; Scaling of reference coordinates, No, All or COM 93refcoord_scaling = No 94 95; GENERATE VELOCITIES FOR STARTUP RUN 96gen-vel = no 97 98; OPTIONS FOR BONDS 99constraints = none 100