## mdp file format

Main Table of Contents | VERSION 4.0
GROMACS homepage | Sun 18 Jan 2009

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
    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

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