| Main Table of Contents | VERSION 3.2 |
| GROMACS homepage | Sun 25 Jan 2004 |
Follow this link for a detailed description of the options.
Below is a sample mdp file. The ordering of the items is not important, but if you enter the same thing twice, the first is used. Dashes and underscores on the left hand side are ignored.
The values of the options are reasonable values for a 1 nanosecond MD run of a protein in a box of water.
title = Yo cpp = /lib/cpp include = -I../top define = integrator = md dt = 0.002 nsteps = 500000 nstxout = 5000 nstvout = 5000 nstlog = 5000 nstenergy = 250 nstxtcout = 250 xtc_grps = Protein energygrps = Protein SOL nstlist = 10 ns_type = grid rlist = 0.8 coulombtype = cut-off rcoulomb = 1.4 rvdw = 0.8 tcoupl = Berendsen tc-grps = Protein SOL tau_t = 0.1 0.1 ref_t = 300 300 Pcoupl = Berendsen tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes gen_temp = 300 gen_seed = 173529 constraints = all-bonds
With this input grompp will produce an mdout.mdp with all the options and descriptions:
; VARIOUS PREPROCESSING OPTIONS = title = Yo cpp = /lib/cpp include = -I../top define = ; RUN CONTROL PARAMETERS = integrator = md ; start time and timestep in ps = tinit = 0 dt = 0.002 nsteps = 500000 ; number of steps for center of mass motion removal = nstcomm = 1 comm-grps = ; LANGEVIN DYNAMICS OPTIONS = ; Temperature, friction coefficient (amu/ps) and random seed = bd-temp = 300 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 ; Frequency of steepest descents steps when doing CG = nstcgsteep = 1000 ; 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 nstenergy = 250 ; Output frequency and precision for xtc file = nstxtcout = 250 xtc-precision = 1000 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = xtc_grps = Protein ; Selection of energy groups = energygrps = Protein SOL ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist = 0.8 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = cut-off rcoulomb-switch = 0 rcoulomb = 1.4 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r = 1 ; Method for doing Van der Waals = vdw-type = Cut-off ; cut-off lengths = rvdw-switch = 0 rvdw = 0.8 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = No ; 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 epsilon_surface = 0 optimize_fft = no ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = tcoupl = Berendsen ; 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 ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; SIMULATED ANNEALING CONTROL = annealing = no ; Time at which temperature should be zero (ps) = zero-temp_time = 0 ; 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 = unconstrained-start = no ; Relative tolerance of shake = shake-tol = 0.0001 ; Highest order in the expansion of the constraint coupling matrix = lincs-order = 4 ; 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 ; NMR refinement stuff = ; Distance restraints type: No, Simple or Ensemble = disre = No ; Force weighting of pairs in one distance restraint: Equal or Conservative = 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 ; Free energy control stuff = free-energy = no init-lambda = 0 delta-lambda = 0 sc-alpha = 0 sc-sigma = 0.3 ; Non-equilibrium MD stuff = acc-grps = accelerate = freezegrps = freezedim = cos-acceleration = 0 energygrp_excl = ; 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 = ; User defined thingies = user1-grps = user2-grps = userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0