1; VARIOUS PREPROCESSING OPTIONS 2; Preprocessor - specify a full path if necessary. 3include = 4define = 5 6; RUN CONTROL PARAMETERS 7integrator = sd 8; Start time and timestep in ps 9tinit = 0 10dt = 0.001 11nsteps = 100000 12; For exact run continuation or redoing part of a run 13init_step = 0 14; mode for center of mass motion removal 15comm-mode = Linear 16; number of steps for center of mass motion removal 17nstcomm = 10 18; group(s) for center of mass motion removal 19comm_grps = 20;system 21 22; LANGEVIN DYNAMICS OPTIONS 23; Friction coefficient (amu/ps) and random seed 24ld-seed = 1993 25 26; OUTPUT CONTROL OPTIONS 27; Output frequency for coords (x), velocities (v) and forces (f) 28nstxout = 0 29nstvout = 0 30nstfout = 0 31; Output frequency for energies to log file and energy file 32nstlog = 100 33nstenergy = 100 34; Output frequency and precision for xtc file 35nstxout-compressed = 100 36compressed-x-precision = 1000 37; This selects the subset of atoms for the xtc file. You can 38; select multiple groups. By default all atoms will be written. 39compressed-x-grps = System ;Protein 40; Selection of energy groups 41energygrps = A B 42 43; NEIGHBORSEARCHING PARAMETERS 44; nblist update frequency 45nstlist = 10 46; ns algorithm (simple or grid) 47ns_type = grid 48; Periodic boundary conditions: xyz (default), no (vacuum) 49; or full (infinite systems only) 50pbc = xyz 51; nblist cut-off 52rlist = 1.5 53 54 55; OPTIONS FOR ELECTROSTATICS AND VDW 56; Method for doing electrostatics 57coulombtype = Cut-off 58rcoulomb-switch = 0 59rcoulomb = 1.5 60; Relative dielectric constant for the medium and the reaction field 61epsilon_r = 1 62epsilon_rf = 1 63; Method for doing Van der Waals 64vdwtype = user 65; cut-off lengths 66rvdw-switch = 0 67rvdw = 1.5 68; Apply long range dispersion corrections for Energy and Pressure 69DispCorr = EnerPres 70; Extension of the potential lookup tables beyond the cut-off 71table-extension = 1.0 72; Seperate tables between energy group pairs 73energygrp_table = A A B B A B 74; Spacing for the PME/PPPM FFT grid 75fourierspacing = 0.12 76; FFT grid size, when a value is 0 fourierspacing will be used 77fourier_nx = 0 78fourier_ny = 0 79fourier_nz = 0 80; EWALD/PME/PPPM parameters 81pme_order = 4 82ewald_rtol = 1e-05 83ewald_geometry = 3d 84epsilon_surface = 0 85 86; OPTIONS FOR WEAK COUPLING ALGORITHMS 87; Temperature coupling 88tcoupl = no 89; Groups to couple separately 90tc-grps = System 91; Time constant (ps) and reference temperature (K) 92tau_t = 1.0 93ref_t = 300 94; Pressure coupling 95Pcoupl = no 96pcoupltype = isotropic 97; Time constant (ps), compressibility (1/bar) and reference P (bar) 98tau_p = 0.5 99compressibility = 4.5e-5 100ref_p = 1.0 101 102 103; GENERATE VELOCITIES FOR STARTUP RUN 104gen_vel = yes 105gen_temp = 300 106gen_seed = -1 107 108; OPTIONS FOR BONDS 109constraints = none 110; Type of constraint algorithm 111constraint_algorithm = LINCS 112; Use successive overrelaxation to reduce the number of shake iterations 113Shake-SOR = no 114; Relative tolerance of shake 115shake-tol = 1e-04 116; Highest order in the expansion of the constraint coupling matrix 117lincs-order = 4 118; Number of iterations in the final step of LINCS. 1 is fine for 119; normal simulations, but use 2 to conserve energy in NVE runs. 120; For energy minimization with constraints it should be 4 to 8. 121lincs_iter = 2 122; Lincs will write a warning to the stderr if in one step a bond 123; rotates over more degrees than 124lincs-warnangle = 30 125; Convert harmonic bonds to morse potentials 126morse = no 127 128; ENERGY GROUP EXCLUSIONS 129; Pairs of energy groups for which all non-bonded interactions are excluded 130energygrp_excl = 131 132