
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.
   * - 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.