mdp file format |
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Main Table of Contents | VERSION 5.0 |
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 last is used (grompp gives you a note when overriding values). 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 nstxout-compressed = 250 compressed-x-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 = nstxout-compressed = 250 compressed-x-precision = 1000 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = compressed-x-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 ; 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