
Section containing the all coarse-graining options
The following table contains the input options for CSG,

.. list-table::
   :header-rows: 1
   :align: center

   * - Property Name
     - Default Value
     - Description
   * - fmatch
     - 
     - Force matching options
   * - fmatch.constrainedLS
     - 
     - | boolean variable: false - simple least squares, true -
       | constrained least squares. For details see the VOTCA paper.
       | Practically, both algorithms give the same results, but
       | simple least squares is faster. If you are a mathematician
       | and you think that a spline can only then be called a
       | spline if it has continuous first and second derivatives,
       | use constrained least squares.
   * - fmatch.dist
     - 1e-5
     - | Accuracy for evaluating the difference in bead positions.
       | Default is 1e-5
   * - fmatch.frames_per_block
     - 
     - | number of frames, being used for block averaging. Atomistic
       | trajectory, specified with --trj option, is divided into
       | blocks and the force matching equations are solved separately
       | for each block. Coarse-grained force-field, which one
       | gets on the output is averaged over those blocks.
   * - inverse
     - 
     - general options for inverse script
   * - inverse.cleanlist
     - 
     -  these files are removed after each iteration
   * - inverse.convergence_check
     - 
     - 
   * - inverse.convergence_check.limit
     - 0
     - lower convergency limit to stop
   * - inverse.convergence_check.type
     - none
     - type of convergence check to do
   * - inverse.dlpoly
     - 
     -  general dlpoly specific options 
   * - inverse.dlpoly.command
     - DLPOLY.Z
     - | command to run dlpoly (name or absolute path or 'mpirun
       | dlpoly' or such)
   * - inverse.dlpoly.topol
     - .dlpf
     -  Name of dlpoly topology file
   * - inverse.dlpoly.traj
     - .dlph
     -  Name of the output dlpoly trajectory file
   * - inverse.dlpoly.checkpoint
     - REVIVE REVCON
     -  Names of the  dlpoly checkpoint files
   * - inverse.dlpoly.table_end
     - 
     - | dlpoly internal grid end point for tabulated non-bonded
       | potentials (applied to all non-bonded)
   * - inverse.dlpoly.table_grid
     - 
     - | dlpoly internal grid number for tabulated non-bonded potentials
       | (applied to all non-bonded)
   * - inverse.dlpoly.bonds
     - 
     - | dlpoly specs for tabulated bonded potentials (applied
       | to all bonds)
   * - inverse.dlpoly.bonds.table_end
     - 
     - dlpoly internal grid end point for tabulated potentials
   * - inverse.dlpoly.bonds.table_grid
     - 
     - dlpoly internal grid number for tabulated potentials
   * - inverse.dlpoly.angles
     - 
     - | dlpoly specs for tabulated bonded potentials (applied
       | to all angles)
   * - inverse.dlpoly.angles.table_grid
     - 
     - dlpoly internal grid number for tabulated potentials
   * - inverse.dlpoly.dihedrals
     - 
     - | dlpoly specs for tabulated bonded potentials (applied
       | to all dihedrals)
   * - inverse.dlpoly.dihedrals.table_grid
     - 
     - dlpoly internal grid number for tabulated potentials
   * - inverse.espresso
     - 
     - 
   * - inverse.espresso.command
     - python3
     - | Command to run espresso (name or absolute path or mpirun
       | espresso..)
   * - inverse.espresso.opts
     - ${script}
     - | option to be given to espresso program, use ${script}
       | in there
   * - inverse.espresso.first_frame
     - 0
     - | trash the given number of frames at the beginning of trajectory
       | 
   * - inverse.espresso.table_bins
     - 
     - espresso internal grid for tabulated potentials
   * - inverse.espresso.traj
     - 
     -  Name of the output Espresso trajectory file
   * - inverse.espressopp
     - 
     - 
   * - inverse.espressopp.command
     - python3
     - | Command to run espresso (name or absolute path or mpirun
       | espresso..)
   * - inverse.espressopp.opts
     - ${script}
     - | option to be given to espresso program, use ${script}
       | in there
   * - inverse.espressopp.first_frame
     - 0
     - | trash the given number of frames at the beginning of trajectory
       | 
   * - inverse.filelist
     - 
     - these files are copied to each iteration step
   * - inverse.gnuplot
     - 
     - 
   * - inverse.gnuplot.bin
     - gnuplot
     - gnuplot binary to use
   * - inverse.gromacs
     - 
     - gromacs specific options 
   * - inverse.gromacs.conf
     - conf.gro
     - Name of the coordinate file read by grompp
   * - inverse.gromacs.conf_out
     - confout.gro
     - Name of the original outcome coordinate written by mdrun
   * - inverse.gromacs.density
     - 
     - 
   * - inverse.gromacs.density.block_length
     - 
     - Length of the block for the error analysis
   * - inverse.gromacs.density.with_errors
     - no
     - calculate error on the density: yes/no
   * - inverse.gromacs.equi_time
     - 0
     - | begin analysis after this time when using gromacs (max
       | of this and first_frame is used)
   * - inverse.gromacs.first_frame
     - 0
     - | trash the given number of frames at the beginning of trajectory
       | (max of this and first_frame is used)
   * - inverse.gromacs.g_energy
     - 
     - 
   * - inverse.gromacs.g_energy.bin
     - /usr/bin/gmx_d energy
     -  Name (or absolute path) of the g_energy binary
   * - inverse.gromacs.g_energy.opts
     - 
     -  Additional options to Gromacs g_energy (e.g. -P 1)
   * - inverse.gromacs.g_energy.pressure
     - 
     -  options for pressure calculation using g_energy
   * - inverse.gromacs.g_energy.pressure.allow_nan
     - no
     -  is nan an allowed result: yes/no
   * - inverse.gromacs.g_energy.topol
     - 
     -  Gromacs binary topol (tpr) file to use by g_energy 
   * - inverse.gromacs.gmxrc
     - 
     - GMXRC to source at the startup
   * - inverse.gromacs.grompp
     - 
     - 
   * - inverse.gromacs.grompp.bin
     - /usr/bin/gmx_d grompp
     -  Name (or absolute path) of the grompp binary
   * - inverse.gromacs.grompp.opts
     - 
     -  Additional options to Gromacs grompp (e.g. -maxwarn 1)
   * - inverse.gromacs.index
     - index.ndx
     -  Gromacs grompp index file to used by grompp
   * - inverse.gromacs.log
     - 
     - | Separate log file for gromacs programs (useful with mdrun
       | -v)
   * - inverse.gromacs.mdp
     - grompp.mdp
     -  Gromacs mdp file to be used by grompp
   * - inverse.gromacs.mdrun
     - 
     - 
   * - inverse.gromacs.mdrun.checkpoint
     - state.cpt
     - Name of the checkpint to use in case of restarted simulation
   * - inverse.gromacs.mdrun.command
     - /usr/bin/gmx_d mdrun
     - | Command to run mdrun (name or absolute path or mpirun
       | mdrun..)
   * - inverse.gromacs.mdrun.multidir
     - 
     -  List of directories for multidir simulations
   * - inverse.gromacs.mdrun.opts
     - 
     -  Additional options to Gromacs mdrun (e.g. -nosum)
   * - inverse.gromacs.pot_max
     - 1000000
     -  cut the potential at this value (gromacs bug) 
   * - inverse.gromacs.pre_simulation
     - no
     - | A pre simulation (e.g. minimization / equilibration )
       | is a simulation with a different mdp/topol/index
   * - inverse.gromacs.pre_simulation.index
     - 
     - | Gromacs grompp index file to used by grompp in the pre
       | simulation
   * - inverse.gromacs.pre_simulation.mdp
     - 
     -  Gromacs mdp file to be used by grompp in the pre simulation
   * - inverse.gromacs.pre_simulation.topol_in
     - 
     - | Gromacs text topol (top) file to use by grompp in the
       | pre simulation
   * - inverse.gromacs.ref
     - 
     - | Options for the case that calculation of reference system
       | is needed
   * - inverse.gromacs.ref.equi_time
     - 0
     - | begin analysis after this time when using gromacs (max
       | of this and first_frame is used)
   * - inverse.gromacs.ref.first_frame
     - 0
     - | trash the given number of frames at the beginning of trajectory
       | (max of this and first_frame is used)
   * - inverse.gromacs.ref.mapping
     - 
     - | Mapping to apply on the coarse-grained topology, use autogenerated
       | ones (cg.inverse.optimizer.mapping.output) and given ones
       | (map other components)
   * - inverse.gromacs.ref.rdf
     - 
     - Contains options for Reference rdf calculation
   * - inverse.gromacs.ref.rdf.opts
     - 
     - Extra options to give to csg_stat (e.g. --nframes 100)
   * - inverse.gromacs.ref.topol
     - 
     - Reference binary topology(global or local path)
   * - inverse.gromacs.ref.traj
     - 
     - Reference trajectory(global or local path)
   * - inverse.gromacs.rdf
     - 
     - 
   * - inverse.gromacs.rdf.block_length
     - 
     - Length of the block for the error analysis
   * - inverse.gromacs.rdf.map
     - 
     - | Space separated list of special mapping file(s) for rdf
       | calculations needed for bonded interactions
   * - inverse.gromacs.rdf.with_errors
     - no
     - calculate error on the rdf: yes/no
   * - inverse.gromacs.table_bins
     - 0.002
     -  grid for gromacs xvg table
   * - inverse.gromacs.table_end
     - 
     - extend the gromacs xvg tables to this value
   * - inverse.gromacs.temp_check
     - yes
     - check kBT against t_ref in mdp file: yes/no
   * - inverse.gromacs.topol_in
     - topol.top
     -  Gromacs text topology (top) file read by grompp
   * - inverse.gromacs.topol
     - topol.tpr
     - | Gromacs binary topology (tpr) file to be written by grompp
       | and used for the simlation
   * - inverse.gromacs.traj
     - traj.xtc
     -  Gromacs trajectory file to use
   * - inverse.gromacs.trjcat
     - 
     - 
   * - inverse.gromacs.trjcat.bin
     - /usr/bin/gmx_d trjcat
     -  Name (or absolute path) of the trjcat binary 
   * - inverse.hoomd-blue
     - 
     - 
   * - inverse.hoomd-blue.command
     - hoomd
     - | Command to run hoomd-blue (name or absolute path or mpirun
       | ..)
   * - inverse.hoomd-blue.opts
     - ${script}
     - | option to be given to hoomd-blue program, use ${script}
       | in there
   * - inverse.imc
     - 
     -  general imc specific options 
   * - inverse.imc.default_reg
     - 0
     - | default magnitude for regularization parameter if not
       | given for the group explicitly, default =0
   * - inverse.lammps
     - 
     -  general lammps specific options 
   * - inverse.lammps.command
     - lmp
     - | command to run lammps (name or absolute path or mpirun
       | lammps..)
   * - inverse.lammps.script
     - 
     -  lammps script to run 
   * - inverse.lammps.opts
     - -in ${script}
     - | option to be given to lammps program, use ${script} in
       | there
   * - inverse.lammps.traj
     - 
     - | trajectory file to be created by lammps, use a format
       | like xyz, which can be read by csg_stat
   * - inverse.lammps.pressure_file
     - 
     - | pressure file generated by lammps, use "fix print" in
       | lammps input (e.g., "fix pressure all print 50 "${mypress}"
       | file lammps.pressure screen no title "LAMMPS_PRESSURE"
       | " ; pressure_file would be lammps.pressure in this example).
       | The title can be anything as VOTCA skips over this line
       | as a header when parsing
   * - inverse.sim_prog
     - 
     -  options, which apply to all simulation programs
   * - inverse.sim_prog.command
     - 
     - | Command to run for the simulation (name or absolute path
       | or mpirun XXX ..)
   * - inverse.sim_prog.conf
     - 
     - | Name of the coordinate file read by the simulation program
       | (if needed)
   * - inverse.sim_prog.conf_out
     - 
     - | Name of the original outcome coordinate written by simulation
       | program (if any)
   * - inverse.sim_prog.equi_time
     - 0
     - | begin analysis after this time (max of this and first_frame
       | is used)
   * - inverse.sim_prog.density
     - 
     - 
   * - inverse.sim_prog.density.block_length
     - 
     - Length of the block for the error analysis
   * - inverse.sim_prog.density.with_errors
     - no
     - calculate error on the density: yes/no
   * - inverse.sim_prog.first_frame
     - 0
     - | trash the given number of frames at the beginning of trajectory
       | (max of this and first_frame is used)
   * - inverse.sim_prog.imc
     - 
     - 
   * - inverse.sim_prog.imc.topol
     - 
     - Special topology file to be used for csg_stat used in imc
   * - inverse.sim_prog.imc.traj
     - 
     - Special trajectory file to be used for csg_stat used in imc
   * - inverse.sim_prog.re
     - 
     - 
   * - inverse.sim_prog.re.topol
     - 
     - Special topology file to be used for csg_reupdate
   * - inverse.sim_prog.re.traj
     - 
     - Special trajectory file to be used for csg_reupdate
   * - inverse.sim_prog.rdf
     - 
     - 
   * - inverse.sim_prog.rdf.block_length
     - 
     - Length of the block for the error analysis
   * - inverse.sim_prog.rdf.map
     - 
     - | Space separated list of special mapping file(s) for rdf
       | calculations needed for bonded interactions
   * - inverse.sim_prog.rdf.topol
     - 
     -  Special topology file to be used for csg_stat
   * - inverse.sim_prog.rdf.traj
     - 
     - Special trajectory file to be used for csg_stat
   * - inverse.sim_prog.rdf.with_errors
     - n
     - calculate error on the rdf: yes/no
   * - inverse.sim_prog.topol
     - 
     - | General topology file to be use if no special one is specified
       | 
   * - inverse.sim_prog.traj
     - 
     -  trajectory file to be created by the simulation program
   * - inverse.sim_prog.script
     - 
     -  simulation script to run (if any)
   * - inverse.sim_prog.opts
     - 
     - | option to be given to simulation program, use ${script}
       | in there
   * - inverse.re
     - 
     - general options for realtive entropy method
   * - inverse.re.csg_reupdate
     - 
     - 
   * - inverse.re.csg_reupdate.opts
     - 
     - options for the csg_reupdate command
   * - inverse.average
     - 
     - 
   * - inverse.average.steps
     - 1
     - | number of steps to be used for average computation. For
       | relative entropy method, these many last iteration steps
       | are used to compute average CG potentials or parameters
       | or both.
   * - inverse.initial_configuration
     - maindir
     - | what initial configuration to use in every step: maindir/laststep/nowhere.
       | 
   * - inverse.iterations_max
     - 
     - do the given number of iterations (-1=inf, 0=only step_000)
   * - inverse.kBT
     - 
     -  kBT in KJ/mol (i.e. XXX K * 0.00831451)
   * - inverse.log_file
     - inverse.log
     - name of the log file
   * - inverse.map
     - 
     - | Special mapping file(s) for rdf calculations needed for
       | bonded interactions
   * - inverse.method
     - 
     - method to be performed: ibi/iie/imc/ft/optimizer
   * - inverse.iie
     - 
     - | general options for the IIE schemes (hncgn/ihnc/hncn/pygn/ipy/pyn)
       | 
   * - inverse.iie.initial_guess
     - 
     - Settings for the initial guess
   * - inverse.iie.initial_guess.method
     - ie
     - Method for the initial potential guess: table/bi/ie
   * - inverse.iie.initial_guess.closure
     - 
     - OZ equation closure in case of method=ie: hnc/py
   * - inverse.iie.initial_guess.ignore_intramolecular_correlation
     - false
     - | If true, the initial guess will ignore the presence of
       | intramolecular correlation in the CG molecule.
   * - inverse.iie.method
     - gauss-newton
     - | Update method to use: gauss-newton/newton/newton-mod.
       | For example closure=hnc + method=gauss-newton will result
       | in the HNCGN method. newton_mod is a modified newton scheme
       | that results in an IBI like expression e.g. IHNC.
   * - inverse.iie.closure
     - hnc
     - OZ equation closure for the IIE update: hnc/py
   * - inverse.iie.ignore_intramolecular_correlation
     - false
     - | If true, the IIE updates (not the initial guess) will
       | ignore the presence of intramolecular correlation in the
       | CG molecule.
   * - inverse.iie.cut_off
     - 
     - | Cut-off used for non-bonded potenitals in MD. Potential
       | will be set to zero beyond this point.
   * - inverse.iie.g_extrap_factor
     - 1.0
     - Lenght factor by which RDF will be extrapolated
   * - inverse.iie.cut_jacobian
     - true
     - | Wether to cut the Jacobian before multiplying with Δg.
       | Only for Newton methods
   * - inverse.iie.densities
     - 
     - | List of densities of the beads, sorted by bead name. TODO:
       | replace by automatic calculation.
   * - inverse.iie.n_intra
     - 
     - | List of n_intra, the number of equal beads, sorted by
       | bead name. TODO: replace by automatic calculation.
   * - inverse.iie.pressure_constraint
     - none
     - Apply pressure constraint. Only for hncgn/pygn
   * - inverse.iie.extrap_near_core
     - power
     - | Method for extrapolation in and close to core region.
       | Valid values are: power (default), constant, none
   * - inverse.iie.fix_near_cut_off
     - full-deriv
     - | Method for fixing discontinuity at end of potential. Valid
       | values are: full-deriv (default), none
   * - inverse.iie.verbose
     - true
     - | Print some info and dump compressed numpy arrays. Valid
       | values are: true (default), false
   * - inverse.optimizer
     - 
     - 
   * - inverse.optimizer.cma
     - 
     - general options for the cma optimizer
   * - inverse.optimizer.cma.eps
     - 
     - standard epsilon, in which the best solution is searched
   * - inverse.optimizer.type
     - 
     - Type of optimizer to be used
   * - inverse.program
     - gromacs
     - simulation package to be used (gromacs/espresso/lammps)
   * - inverse.restart_file
     - restart_points.log
     - Name of the restart file in case a step has to be resumed
   * - inverse.dist_min
     - 1e-10
     - | minimal value for the rdf to consider for initial guess
       | of the potential)
   * - inverse.scriptpath
     - 
     - | list of directories for user scripts (e.g. $PWD) separated
       | by a colon (like PATH)
   * - inverse.simulation
     - 
     - simulation options 
   * - inverse.simulation.background
     - no
     - tells csg_inverse that simulation was send to the backgroud
   * - inverse.simulation.tasks
     - auto
     - number of threads to use for csg_stat
   * - inverse.scale
     - 
     - update scaling factor for the relative entropy update
   * - nbsearch
     - grid
     - Grid search algorithm, simple (N square search) or grid
   * - bonded
     - 
     - | Interaction specific option for bonded interactions, see
       | the cg.non-bonded section for all options
   * - bonded.dlpoly
     - 
     - 
   * - bonded.dlpoly.header
     - 
     - | Header of the interaction in dlpoly TABBND or TABANG file.
       | The header should be a unique set of the interaction-site
       | names, and these should match the corresponding names
       | specified in the mapping file.
   * - bonded.name
     - 
     - | Name of the bonded interaction. The name can be arbitrary
       | but should be unique. For bonded interactions, this should
       | match the name specified in the mapping file.
   * - bonded.periodic
     - 0
     - | set to 1 when calculating bond dihedral potentials with
       | csg_fmatch -> enforces periodicity of potential. (default
       | is 0)
   * - non-bonded
     - 
     - Interaction specific option for non-bonded interactions
   * - non-bonded.dlpoly
     - 
     - 
   * - non-bonded.dlpoly.header
     - 
     - | Header of the interaction in dlpoly TABLE file. The header
       | should be a unique pair of the interaction-site names,
       | and these should match the corresponding names specified
       | in the mapping file.
   * - non-bonded.name
     - 
     - | Name of the interaction. The name can be arbitrary but
       | should be unique. For bonded interactions, this should
       | match the name specified in the mapping file.
   * - non-bonded.type1
     - 
     - **Bead** type 1 of non-bonded interaction.
   * - non-bonded.type2
     - 
     - **Bead** type 2 of non-bonded interaction.
   * - non-bonded.bondtype
     - 
     - | Internal alias for "non-bonded" or "bonded", set automatically
       | 
   * - non-bonded.min
     - 
     - | Lower bound of interval for potential table in which calculations
       | are performed. Should be set based on reference distributions.
   * - non-bonded.max
     - 
     - | Upper bound of interval for potential table in which calculations
       | are performed. Should be set based on reference distributions.
   * - non-bonded.step
     - 
     - | Step size of interval for potential table in which calculations
       | are performed. If step site is too small, lots of statistics
       | is needed ( long runs ). If it's too big, features in
       | the distribtuion/potentials might get lost.
   * - non-bonded.fmatch
     - 
     - Force matching options
   * - non-bonded.fmatch.min
     - 
     - | Minimum value of interval for distribution sampled in
       | atomistic MD simulation. One can get this number by looking
       | at the distribution function for this interaction. For
       | non-bonded interactions it's the distance to the rdf start.
       | For CG bonds and angles the variable has the similar meaning
       | ( note, that for angles it is specified in radians ).
   * - non-bonded.fmatch.max
     - 
     - | Maximum value of interval for distribution sampled in
       | atomistic MD simulation. One can get this number by looking
       | at the distribution function for this interaction. For
       | non-bonded interactions it's the cut-off of the interaction.
   * - non-bonded.fmatch.step
     - 
     - | grid spacing for the spline, which represents the interaction.
       | This parameter should not be too big, otherwise you might
       | lose some features of the interaction potential, and not
       | too small either, otherwise you will have unsampled bins
       | which result in an ill-defined equation system and NaNs
       | in the output.
   * - non-bonded.fmatch.out_step
     - 
     - | Grid spacing for the output grid. Normally, one wants
       | to have this parameter smaller than fmatch.step, to have
       | a smooth curve, without additional spline interpolation.
       | As a rule of thumb we normally use fmatch.out_step which
       | is approximately 5 times smaller than fmatch.step.
   * - non-bonded.re
     - 
     - Relative entropy options
   * - non-bonded.re.function
     - 
     - | Functional form for the potential. Available functional
       | forms: lj126 (Lennard-Jones 12-6), ljg (Lennard-Jones
       | 12-6 plus Gaussian), and cbspl (uniform cubic B-splines).
   * - non-bonded.re.cbspl
     - 
     - options specific to cbspl function form
   * - non-bonded.re.cbspl.nknots
     - 
     - | Number of knot values to be used for the cbspl functional
       | form. Uniform grid size of the CBSPL depends on this parameter;
       | for fixed potential range more the nknots smaller the
       | grid spacing. Make sure grid spacing is sufficiently large
       | and enough CG simulation steps are performed such that
       | the bins at distance greater than the minimum distance
       | are sampled sufficiently otherwise ill-defined system
       | of equation would give NaNs in the output.
   * - non-bonded.inverse
     - 
     - Contains all information relevant to iterative process
   * - non-bonded.inverse.target
     - 
     - | target distribution (e.g. rdf) which is tried to match
       | during iterations to match
   * - non-bonded.inverse.p_target
     - 
     - pressure contribution of this interaction
   * - non-bonded.inverse.particle_dens
     - 
     - | particle density of this species (for wjk pressure correction)
       | 
   * - non-bonded.inverse.do_potential
     - 1
     - | Update cycle for the potential update. 1 means update,
       | 0 don't update. 1 1 0 means update 2 iterations, then
       | don't one iteration update, then repeat.
   * - non-bonded.inverse.espresso
     - 
     - Espresso specific options for this interations
   * - non-bonded.inverse.espresso.table
     - 
     - | Name of file for tabulated potential of this interaction.
       | This fill will be created from the internal tabulated
       | potential format in every step. Note, though, that the
       | original espresso script needs to contain the name of
       | that table as the tabulated interaction (see tutorial
       | methanol ibi_espresso for details).
   * - non-bonded.inverse.espressopp
     - 
     - Espresso++ specific options for this interations
   * - non-bonded.inverse.hoomd-blue
     - 
     - HOOMD-blue specific options for this interations
   * - non-bonded.inverse.gromacs
     - 
     - Gromacs specific options for this interations
   * - non-bonded.inverse.gromacs.table
     - 
     - | Name of file for tabulated potential of this interaction.
       | This fill will be created from the internal tabulated
       | potential format in every step.
   * - non-bonded.inverse.sim_prog
     - 
     - | interaction specific options, which apply to all simulation
       | programs
   * - non-bonded.inverse.sim_prog.table
     - 
     - | Name of file for tabulated potential of this interaction.
       | This fill will be created from the internal tabulated
       | potential format in every step. Note, though, that the
       | original simulation script needs to contain the name of
       | that table as the tabulated interaction (see tutorial
       | methanol ibi_espresso for details).
   * - non-bonded.inverse.sim_prog.table_begin
     - 
     - | Start of the tabulated potential of this interaction.
       | (Automatic for gromacs)
   * - non-bonded.inverse.sim_prog.table_end
     - 
     - | End of the tabulated potential of this interaction. (Automatic
       | for gromacs)
   * - non-bonded.inverse.sim_prog.table_left_extrapolation
     - 
     - | Extrapolation function to use on the left. Default: exponential(non-bonded),
       | linear (bonded), Options: constant linear quadratic exponential
       | sasha
   * - non-bonded.inverse.sim_prog.table_right_extrapolation
     - 
     - | Extrapolation function to use on the right. Default: constant(non-bonded),
       | linear (bonded), Options: constant linear quadratic exponential
       | sasha
   * - non-bonded.inverse.sim_prog.table_bins
     - 
     - | Binszie of the tabulated potential of this interaction.
       | (gromacs uses a non interaction specific option)
   * - non-bonded.inverse.imc
     - 
     - section containing inverse monte carlo specific options.
   * - non-bonded.inverse.imc.group
     - 
     - | Group of interaction. Cross-correlations of all members
       | of a group are taken into account for calculating the
       | update. If no cross correlations should be calculated,
       | interactions have to be put into different groups. Group
       | 'none' is completely ignored and update_potential needs
       | to be zero for the respective interactions.
   * - non-bonded.inverse.lammps
     - 
     - lammps specific options for this interations
   * - non-bonded.inverse.lammps.scale
     - 1
     - | x-axis scaling factor for the potential output, can be
       | used to convert VOTCA units, nm, to other units, e.g.
       | angstroms
   * - non-bonded.inverse.lammps.table
     - 
     - | Name of file for tabulated potential of this interaction.
       | This fill will be created from the internal tabulated
       | potential format in every step. Note, though, that the
       | lammps script needs to contain the name of that table
       | as the tabulated interaction and the interaction is stored
       | in the VOTCA section of the file..
   * - non-bonded.inverse.lammps.y_scale
     - 1
     - | y-axis scaling factor for the potential output, can be
       | used to convert VOTCA units, kJ/mol, to other units, e.g.
       | kcal/mol
   * - non-bonded.inverse.post_add
     - 
     - | Additional post processing of U after dU added to potential.
       | This is a list of scripts separated by spaces which are
       | called. See section on iterative framework for details.
   * - non-bonded.inverse.post_add_options
     - 
     - Contains all options of post add scripts
   * - non-bonded.inverse.post_add_options.compress
     - 
     - Contains all options of the postadd compress sripts
   * - non-bonded.inverse.post_add_options.compress.filelist
     - 
     - Files to be compressed
   * - non-bonded.inverse.post_add_options.compress.program_opts
     - -9
     - Option to give to the compression command
   * - non-bonded.inverse.post_add_options.compress.program
     - gzip
     - Compression command to run
   * - non-bonded.inverse.post_add_options.convergence
     - 
     - 
   * - non-bonded.inverse.post_add_options.convergence.weight
     - 1
     - | weight factors for the convergence of this interaction,
       | should be a list of same length as inverse.post_add_options.convergence.what
   * - non-bonded.inverse.post_add_options.convergence.what
     - dist
     - list from what to calc the convergence: dist pot, ..
   * - non-bonded.inverse.post_add_options.convergence.base
     - tgt
     - | what base values to be used to compute convergene error:
       | tgt, cur, ..
   * - non-bonded.inverse.post_add_options.convergence.norm
     - 1
     - | which norm to use to compute error: 1 first norm, 2 second
       | norm
   * - non-bonded.inverse.post_add_options.copyback
     - 
     - Contains all options of the postadd copyback sripts
   * - non-bonded.inverse.post_add_options.copyback.filelist
     - 
     - File to be copied to back to maindir
   * - non-bonded.inverse.post_add_options.overwrite
     - 
     - Contains all options of the overwrite postadd scripts
   * - non-bonded.inverse.post_add_options.overwrite.do
     - 1
     - | Cycle for overwrite postadd script (1 do, 0 do not) like
       | do_potential.
   * - non-bonded.inverse.post_add_options.plot
     - 
     - Contains all options of the plot postadd scripts
   * - non-bonded.inverse.post_add_options.plot.fd
     - 8
     - | file descriptor to use, make it unique if you want to
       | plot multiple things
   * - non-bonded.inverse.post_add_options.plot.gnuplot_opts
     - 
     - | extra options to give to gnuplot_bin like -persist or
       | -geometry
   * - non-bonded.inverse.post_add_options.plot.kill
     - 
     - | kill all processes with that name before ploting (e.g.
       | gnuplot_x11), this is more reliable than using named pipes
   * - non-bonded.inverse.post_add_options.plot.script
     - 
     - plot script to give to gnuplot
   * - non-bonded.inverse.post_add_options.average
     - 
     - 
   * - non-bonded.inverse.post_add_options.average.what
     - 
     - | list for which averages of last few steps are to computed:
       | param, pot, ... For relative entropy method, specify param
       | before pot.
   * - non-bonded.inverse.post_update
     - 
     - | Additional post-processing of dU before added to potential.
       | This is a list of scripts separated by spaces which are
       | called. See section on iterative framework for details.
   * - non-bonded.inverse.post_update_options
     - 
     - Contains all options of post update scripts
   * - non-bonded.inverse.post_update_options.cibi
     - 
     - | Contains all options of the Kirkwood-Buff integral corrections
       | scripts
   * - non-bonded.inverse.post_update_options.cibi.do
     - 1
     - | Update cycle for the Kirkwood-Buff integral correction
       | (1 do, 0 do not). To do the correction every third step
       | specify "0 0 1", similar to do_potential
   * - non-bonded.inverse.post_update_options.cibi.kbint_with_errors
     - no
     - calculate errors on the Kirkwood-Buff integral: yes/no
   * - non-bonded.inverse.post_update_options.extrapolate
     - 
     - 
   * - non-bonded.inverse.post_update_options.extrapolate.points
     - 5
     - | Number of point to calculate the average from for the
       | extrapolation
   * - non-bonded.inverse.post_update_options.ibi
     - 
     - Contains all options of the IBI post-update script
   * - non-bonded.inverse.post_update_options.ibi.do
     - 1
     - | Update cycle for the IBI post-update (1 do, 0 do not).
       | To do the post-update every third step specify "0 0 1",
       | similar to do_potential
   * - non-bonded.inverse.post_update_options.kbibi
     - 
     - | Contains all options of the Kirkwood-Buff ramp corrections
       | scripts
   * - non-bonded.inverse.post_update_options.kbibi.do
     - 1
     - | Update cycle for the Kirkwood-Buff ramp correction (1
       | do, 0 do not). To do the correction every third step specify
       | "0 0 1", similar to do_potential
   * - non-bonded.inverse.post_update_options.kbibi.factor
     - 
     - scaling factor for the ramp correction
   * - non-bonded.inverse.post_update_options.kbibi.kbint_with_errors
     - no
     - calculate errors on the Kirkwood-Buff integral: yes/no
   * - non-bonded.inverse.post_update_options.kbibi.r_ramp
     - 
     - cutoff of the ramp
   * - non-bonded.inverse.post_update_options.kbibi.start
     - 
     - | Where to start averaging the Kirkwood-Buff integral for
       | the ramp
   * - non-bonded.inverse.post_update_options.kbibi.stop
     - 
     - | Where to stop averaging the Kirkwood-Buff integral for
       | the ramp
   * - non-bonded.inverse.post_update_options.lj
     - 
     - Contains all options of the Lennard-Jones potential update
   * - non-bonded.inverse.post_update_options.lj.c6
     - 
     - The c6 value for the extra LJ potential
   * - non-bonded.inverse.post_update_options.lj.c12
     - 
     - The c12 value for the extra LJ potential
   * - non-bonded.inverse.post_update_options.pressure
     - 
     - Contains all options of the pressure correction scripts
   * - non-bonded.inverse.post_update_options.pressure.do
     - 1
     - | Update cycle for the pressure correction (1 do, 0 do not).
       | To do pressure correction every third step specify "0
       | 0 1", similar to do_potential
   * - non-bonded.inverse.post_update_options.pressure.simple
     - 
     - Contains all options of the simple pressure correction
   * - non-bonded.inverse.post_update_options.pressure.simple.max_A
     - 0.1
     - maximum prefactor in units of kBT
   * - non-bonded.inverse.post_update_options.pressure.simple.scale
     - 
     - slope of the simple pressure correction
   * - non-bonded.inverse.post_update_options.pressure.ptype
     - 
     - Generic Pressure correction options
   * - non-bonded.inverse.post_update_options.pressure.ptype.max_A
     - 
     - maximum prefactor in units of kBT
   * - non-bonded.inverse.post_update_options.pressure.ptype.scale
     - 
     - slope of the pressure correction
   * - non-bonded.inverse.post_update_options.pressure.type
     - simple
     - Pressure correction type, can be simple or wjk
   * - non-bonded.inverse.post_update_options.pressure.wjk
     - 
     - Contains all options of the wjk pressure correction
   * - non-bonded.inverse.post_update_options.pressure.wjk.max_A
     - 0.1
     - maximum prefactor in units of kBT
   * - non-bonded.inverse.post_update_options.pressure.wjk.scale
     - 1.0
     - extra scaling factor of pressure wjk correction
   * - non-bonded.inverse.post_update_options.scale
     - 1.0
     - scale factor for the update
   * - non-bonded.inverse.post_update_options.smooth
     - 
     - Contains all options of the post_update smooth script
   * - non-bonded.inverse.post_update_options.smooth.iterations
     - 1
     - number of triangular smooth to be performed
   * - non-bonded.inverse.post_update_options.splinesmooth
     - 
     - Contains all options of the post_update spline smooth script
   * - non-bonded.inverse.post_update_options.splinesmooth.step
     - 
     - grid spacing for spline fit when doing spline smoothing
   * - non-bonded.inverse.optimizer
     - 
     - 
   * - non-bonded.inverse.optimizer.density
     - 
     - | Contains all options for the density calculation of the
       | optimizer
   * - non-bonded.inverse.optimizer.density.axis
     - x
     - Axis along which the density is calculated
   * - non-bonded.inverse.optimizer.density.min
     - 
     - | Lower bound of interval in which density calculation is
       | performed.
   * - non-bonded.inverse.optimizer.density.max
     - 
     - | Upper bound of interval in which density calculation is
       | performed.
   * - non-bonded.inverse.optimizer.density.step
     - 
     - | Step size of interval in which density calculation is
       | performed.
   * - non-bonded.inverse.optimizer.density.scale
     - 1.0
     - Scaling factor for density
   * - non-bonded.inverse.optimizer.density.molname
     - *
     - The molname of this interaction
   * - non-bonded.inverse.optimizer.density.target
     - 
     - Filename of the target denstiy distribution in the maindir
   * - non-bonded.inverse.optimizer.function
     - 
     - Functional form of the interaction, using parameters in here
   * - non-bonded.inverse.optimizer.functionfile
     - 
     - | If the function is very complicated it can be defined
       | in this files, which is used as an header
   * - non-bonded.inverse.optimizer.mapping
     - 
     - option related to mapping changes
   * - non-bonded.inverse.optimizer.mapping.change
     - no
     - Does the mapping change in optimization: yes/no
   * - non-bonded.inverse.optimizer.mapping.output
     - no
     - Output file name for mapping
   * - non-bonded.inverse.optimizer.mapping.template
     - 
     - template for the mapping optimization
   * - non-bonded.inverse.optimizer.parameters
     - 
     - | Parameters to be fitted by the optimizer for this interaction.
       | Note that the parameter names are global
   * - non-bonded.inverse.optimizer.pressure
     - 
     - | Contains all options for the pressure calculation of the
       | optimizer
   * - non-bonded.inverse.optimizer.pressure.undef
     - 
     - | Pressure to use if pressure from the simulation was nan
       | (use a big number)
   * - non-bonded.inverse.optimizer.rdf
     - 
     - | Contains all options for the rdf calculation of the optimizer
       | 
   * - non-bonded.inverse.optimizer.rdf.target
     - 
     - Filename of the target rdf in the maindir
   * - non-bonded.inverse.optimizer.rdf.weight
     - 
     - | Weighting function for calculating the convergency of
       | the rdf
   * - non-bonded.inverse.optimizer.rdf.weightfile
     - 
     - | File with the weighting function definition calculating
       | the rdf
   * - non-bonded.inverse.optimizer.targets
     - rdf
     - Targets to be fitted by the optimizer
   * - non-bonded.inverse.optimizer.target_weights
     - 1
     - | Weight of the targets, amount has to be the same as of
       | targets