1; 2; File 'mdout.mdp' was generated 3; By user: mark (1302) 4; On host: amd2 5; At date: Wed Dec 19 13:44:25 2012 6; 7 8; VARIOUS PREPROCESSING OPTIONS 9; Preprocessor information: use cpp syntax. 10; e.g.: -I/home/joe/doe -I/home/mary/roe 11include = 12; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) 13define = -DPOSRES 14 15; RUN CONTROL PARAMETERS 16integrator = md 17; Start time and timestep in ps 18tinit = 0.0 19dt = 0.001 20nsteps = 20 21; For exact run continuation or redoing part of a run 22init-step = 0 23; Part index is updated automatically on checkpointing (keeps files separate) 24simulation-part = 1 25 26; OUTPUT CONTROL OPTIONS 27; Output frequency for coords (x), velocities (v) and forces (f) 28nstxout = 20 29nstvout = 20 30nstfout = 20 31; Output frequency for energies to log file and energy file 32nstlog = 20 33nstcalcenergy = 1 34nstenergy = 1 35 36; NEIGHBORSEARCHING PARAMETERS 37; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs) 38cutoff-scheme = Verlet 39; nblist update frequency 40nstlist = 10 41; Periodic boundary conditions: xyz, no, xy 42pbc = xyz 43periodic-molecules = no 44; Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom, 45; a value of -1 means: use rlist 46verlet-buffer-tolerance = 0.005 47; nblist cut-off 48rlist = 1.0 49 50; OPTIONS FOR ELECTROSTATICS AND VDW 51; Method for doing electrostatics 52coulomb_type = pme 53coulomb-modifier = Potential-shift-Verlet 54rcoulomb_switch = 0.99 55rcoulomb = 1.0 56; Relative dielectric constant for the medium and the reaction field 57epsilon_r = 1.0 58epsilon-rf = 0 59; Method for doing Van der Waals 60vdw_type = Cut-off 61vdw-modifier = Force-switch 62; cut-off lengths 63rvdw_switch = 0.8 64rvdw = 1 65; Apply long range dispersion corrections for Energy and Pressure 66dispcorr = enerpres 67; Extension of the potential lookup tables beyond the cut-off 68table-extension = 1 69; Seperate tables between energy group pairs 70energygrp-table = 71; Spacing for the PME/PPPM FFT grid 72fourierspacing = 0.12 73 74; EWALD/PME/PPPM parameters 75pme-order = 4 76ewald_rtol = 1e-6 77ewald-geometry = 3d 78epsilon-surface = 0 79 80; OPTIONS FOR WEAK COUPLING ALGORITHMS 81; Temperature coupling 82tcoupl = berendsen 83nsttcouple = 1 84; Groups to couple separately 85tc-grps = system 86; Time constant (ps) and reference temperature (K) 87tau_t = 1.0 88ref_t = 298 89; pressure coupling 90Pcoupl = no 91 92; GENERATE VELOCITIES FOR STARTUP RUN 93gen-vel = no 94 95; OPTIONS FOR BONDS 96constraints = h-bonds 97; Type of constraint algorithm 98constraint-algorithm = Lincs 99; Do not constrain the start configuration 100continuation = no 101; Highest order in the expansion of the constraint coupling matrix 102lincs-order = 8 103; Number of iterations in the final step of LINCS. 1 is fine for 104; normal simulations, but use 2 to conserve energy in NVE runs. 105; For energy minimization with constraints it should be 4 to 8. 106lincs-iter = 2 107; Lincs will write a warning to the stderr if in one step a bond 108; rotates over more degrees than 109lincs-warnangle = 30 110; Convert harmonic bonds to morse potentials 111morse = no 112 113; ENERGY GROUP EXCLUSIONS 114; Pairs of energy groups for which all non-bonded interactions are excluded 115energygrp-excl = 116 117; Free energy variables 118free-energy = yes 119couple_moltype = 120couple_lambda0 = vdw-q 121couple_lambda1 = vdw-q 122init-lambda-state = 12 123nstdhdl = 5 124fep-lambdas = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.00 0.0 0.00 0.0 0.00 0.0 0.0 125mass-lambdas = 126coul-lambdas = 0.0 0.1 0.2 0.3 0.5 0.7 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.0 127vdw-lambdas = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.65 0.7 0.75 0.8 0.85 0.9 1.0 128bonded-lambdas = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.65 0.7 0.75 0.8 0.85 0.9 1.0 129restraint-lambdas = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 0.9 0.9 0.9 0.90 0.9 1.00 1.0 1.00 1.0 1.0 130temperature-lambdas = 131init-lambda-weights = 132dhdl-print-energy = no 133sc-alpha = 0.5 134sc-power = 1 135sc-r-power = 6 136sc-sigma = 0.3 137sc-coul = no 138separate-dhdl-file = no 139dhdl-derivatives = yes 140dh_hist_size = 0 141dh_hist_spacing = 0.1 142 143