## mdp file format

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

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