--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Bool Name="Error parsing mdp file">false</Bool>
+ <String Name="OutputMdpFile">
+; VARIOUS PREPROCESSING OPTIONS
+; Preprocessor information: use cpp syntax.
+; e.g.: -I/home/joe/doe -I/home/mary/roe
+include =
+; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)
+define = -DBOOL -DVAR=VALUE
+
+; RUN CONTROL PARAMETERS
+integrator = md
+; Start time and timestep in ps
+tinit = 0
+dt = 0.001
+nsteps = 0
+; For exact run continuation or redoing part of a run
+init-step = 0
+; Part index is updated automatically on checkpointing (keeps files separate)
+simulation-part = 1
+; mode for center of mass motion removal
+comm-mode = Linear
+; number of steps for center of mass motion removal
+nstcomm = 100
+; group(s) for center of mass motion removal
+comm-grps =
+
+; LANGEVIN DYNAMICS OPTIONS
+; Friction coefficient (amu/ps) and random seed
+bd-fric = 0
+ld-seed = -1
+
+; ENERGY MINIMIZATION OPTIONS
+; Force tolerance and initial step-size
+emtol = 10
+emstep = 0.01
+; Max number of iterations in relax-shells
+niter = 20
+; Step size (ps^2) for minimization of flexible constraints
+fcstep = 0
+; Frequency of steepest descents steps when doing CG
+nstcgsteep = 1000
+nbfgscorr = 10
+
+; TEST PARTICLE INSERTION OPTIONS
+rtpi = 0.05
+
+; OUTPUT CONTROL OPTIONS
+; Output frequency for coords (x), velocities (v) and forces (f)
+nstxout = 0
+nstvout = 0
+nstfout = 0
+; Output frequency for energies to log file and energy file
+nstlog = 1000
+nstcalcenergy = 100
+nstenergy = 1000
+; Output frequency and precision for .xtc file
+nstxout-compressed = 0
+compressed-x-precision = 1000
+; This selects the subset of atoms for the compressed
+; trajectory file. You can select multiple groups. By
+; default, all atoms will be written.
+compressed-x-grps =
+; Selection of energy groups
+energygrps =
+
+; NEIGHBORSEARCHING PARAMETERS
+; cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)
+cutoff-scheme = Verlet
+; nblist update frequency
+nstlist = 10
+; ns algorithm (simple or grid)
+ns-type = Grid
+; Periodic boundary conditions: xyz, no, xy
+pbc = xyz
+periodic-molecules = no
+; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,
+; a value of -1 means: use rlist
+verlet-buffer-tolerance = 0.005
+; nblist cut-off
+rlist = 1
+; long-range cut-off for switched potentials
+
+; OPTIONS FOR ELECTROSTATICS AND VDW
+; Method for doing electrostatics
+coulombtype = Cut-off
+coulomb-modifier = Potential-shift-Verlet
+rcoulomb-switch = 0
+rcoulomb = 1
+; Relative dielectric constant for the medium and the reaction field
+epsilon-r = 1
+epsilon-rf = 0
+; Method for doing Van der Waals
+vdw-type = Cut-off
+vdw-modifier = Potential-shift-Verlet
+; cut-off lengths
+rvdw-switch = 0
+rvdw = 1
+; Apply long range dispersion corrections for Energy and Pressure
+DispCorr = No
+; Extension of the potential lookup tables beyond the cut-off
+table-extension = 1
+; Separate tables between energy group pairs
+energygrp-table =
+; 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
+ewald-rtol-lj = 0.001
+lj-pme-comb-rule = Geometric
+ewald-geometry = 3d
+epsilon-surface = 0
+
+; IMPLICIT SOLVENT ALGORITHM
+implicit-solvent = No
+
+; GENERALIZED BORN ELECTROSTATICS
+; Algorithm for calculating Born radii
+gb-algorithm = Still
+; Frequency of calculating the Born radii inside rlist
+nstgbradii = 1
+; Cutoff for Born radii calculation; the contribution from atoms
+; between rlist and rgbradii is updated every nstlist steps
+rgbradii = 1
+; Dielectric coefficient of the implicit solvent
+gb-epsilon-solvent = 80
+; Salt concentration in M for Generalized Born models
+gb-saltconc = 0
+; Scaling factors used in the OBC GB model. Default values are OBC(II)
+gb-obc-alpha = 1
+gb-obc-beta = 0.8
+gb-obc-gamma = 4.85
+gb-dielectric-offset = 0.009
+sa-algorithm = Ace-approximation
+; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
+; The value -1 will set default value for Still/HCT/OBC GB-models.
+sa-surface-tension = -1
+
+; OPTIONS FOR WEAK COUPLING ALGORITHMS
+; Temperature coupling
+tcoupl = No
+nsttcouple = -1
+nh-chain-length = 10
+print-nose-hoover-chain-variables = no
+; Groups to couple separately
+tc-grps =
+; Time constant (ps) and reference temperature (K)
+tau-t =
+ref-t =
+; pressure coupling
+pcoupl = No
+pcoupltype = Isotropic
+nstpcouple = -1
+; Time constant (ps), compressibility (1/bar) and reference P (bar)
+tau-p = 1
+compressibility =
+ref-p =
+; Scaling of reference coordinates, No, All or COM
+refcoord-scaling = No
+
+; OPTIONS FOR QMMM calculations
+QMMM = no
+; Groups treated Quantum Mechanically
+QMMM-grps =
+; QM method
+QMmethod =
+; QMMM scheme
+QMMMscheme = normal
+; QM basisset
+QMbasis =
+; QM charge
+QMcharge =
+; QM multiplicity
+QMmult =
+; Surface Hopping
+SH =
+; CAS space options
+CASorbitals =
+CASelectrons =
+SAon =
+SAoff =
+SAsteps =
+; Scale factor for MM charges
+MMChargeScaleFactor = 1
+
+; SIMULATED ANNEALING
+; Type of annealing for each temperature group (no/single/periodic)
+annealing =
+; Number of time points to use for specifying annealing in each group
+annealing-npoints =
+; List of times at the annealing points for each group
+annealing-time =
+; Temp. at each annealing point, for each group.
+annealing-temp =
+
+; GENERATE VELOCITIES FOR STARTUP RUN
+gen-vel = no
+gen-temp = 300
+gen-seed = -1
+
+; OPTIONS FOR BONDS
+constraints = none
+; Type of constraint algorithm
+constraint-algorithm = Lincs
+; Do not constrain the start configuration
+continuation = no
+; Use successive overrelaxation to reduce the number of shake iterations
+Shake-SOR = no
+; Relative tolerance of shake
+shake-tol = 0.0001
+; Highest order in the expansion of the constraint coupling matrix
+lincs-order = 4
+; Number of iterations in the final step of LINCS. 1 is fine for
+; normal simulations, but use 2 to conserve energy in NVE runs.
+; For energy minimization with constraints it should be 4 to 8.
+lincs-iter = 1
+; 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
+
+; ENERGY GROUP EXCLUSIONS
+; Pairs of energy groups for which all non-bonded interactions are excluded
+energygrp-excl =
+
+; WALLS
+; Number of walls, type, atom types, densities and box-z scale factor for Ewald
+nwall = 0
+wall-type = 9-3
+wall-r-linpot = -1
+wall-atomtype =
+wall-density =
+wall-ewald-zfac = 3
+
+; COM PULLING
+pull = no
+
+; AWH biasing
+awh = no
+
+; ENFORCED ROTATION
+; Enforced rotation: No or Yes
+rotation = no
+
+; Group to display and/or manipulate in interactive MD session
+IMD-group =
+
+; NMR refinement stuff
+; Distance restraints type: No, Simple or Ensemble
+disre = No
+; Force weighting of pairs in one distance restraint: Conservative or Equal
+disre-weighting = Conservative
+; 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
+; Orientation restraints: No or Yes
+orire = no
+; Orientation restraints force constant and tau for time averaging
+orire-fc = 0
+orire-tau = 0
+orire-fitgrp =
+; Output frequency for trace(SD) and S to energy file
+nstorireout = 100
+
+; Free energy variables
+free-energy = no
+couple-moltype =
+couple-lambda0 = vdw-q
+couple-lambda1 = vdw-q
+couple-intramol = no
+init-lambda = -1
+init-lambda-state = -1
+delta-lambda = 0
+nstdhdl = 50
+fep-lambdas =
+mass-lambdas =
+coul-lambdas =
+vdw-lambdas =
+bonded-lambdas =
+restraint-lambdas =
+temperature-lambdas =
+calc-lambda-neighbors = 1
+init-lambda-weights =
+dhdl-print-energy = no
+sc-alpha = 0
+sc-power = 1
+sc-r-power = 6
+sc-sigma = 0.3
+sc-coul = no
+separate-dhdl-file = yes
+dhdl-derivatives = yes
+dh_hist_size = 0
+dh_hist_spacing = 0.1
+
+; Non-equilibrium MD stuff
+acc-grps =
+accelerate =
+freezegrps =
+freezedim =
+cos-acceleration = 0
+deform =
+
+; simulated tempering variables
+simulated-tempering = no
+simulated-tempering-scaling = geometric
+sim-temp-low = 300
+sim-temp-high = 300
+
+; Ion/water position swapping for computational electrophysiology setups
+; Swap positions along direction: no, X, Y, Z
+swapcoords = no
+adress = no
+
+; User defined thingies
+user1-grps =
+user2-grps =
+userint1 = 0
+userint2 = 0
+userint3 = 0
+userint4 = 0
+userreal1 = 0
+userreal2 = 0
+userreal3 = 0
+userreal4 = 0
+; Electric fields
+; Format for electric-field-x, etc. is: four real variables:
+; amplitude (V/nm), frequency omega (1/ps), time for the pulse peak (ps),
+; and sigma (ps) width of the pulse. Omega = 0 means static field,
+; sigma = 0 means no pulse, leaving the field to be a cosine function.
+electric-field-x = 0 0 0 0
+electric-field-y = 0 0 0 0
+electric-field-z = 0 0 0 0
+</String>
+</ReferenceData>