RDF/potential record:

&RDF ... &EndRDF
or
&Potential ... &EndPotential

Each individual record specifies one RDF/potential, providing information the CG atom types, range, number of points and the data-table with actual values. A record can be also included from a separate file. Every record consists of specifications, data table (&Table...&EndTable) and optional include section (&IncludePotential...&EndIncludePotential).

Name

- Name of the RDF/potential record. Is used as a comment line

Type

- Type of the record. Can be NB, B, A, i.e. non-bonded, pairwise bond, angle-bending bond, respectively

Min, Max

- Range (in Å) where the record is defined

NPoints

- Number of points in the record. Note, that for the core region of RDF, which has zero values and often omitted, the Min value is typically not zero

AtomTypes

- For NB-record, specifies the pair of bead/atom types which are involved in the interaction.

MolType

- For B- or A-record, specifies molecular type the bond belongs to.

BondNumber

- For B- or A-record, specifies a relative number of bond to which this record belongs. Note that bonds are indexed locally, with respect to the molecular type, the same way as in the corresponding mcm-file for the given molecular type

NPairs or NTriplets

- Number of atom pairs (triplets) involved in the bond (B- or A-bond)

Pairs or Triplets

- List of atom pairs (triplets) involved in the bond. Pairs/Triplets are comma separated, and atom numbers are separated by dash symbol (-) withing each pair/triplet. For triplets, atom numbers are specified in a direct way, so the central atom of the triplet is a central atom of the angle. Atoms are numbered locally, with respect to the molecular type, same way as in the corresponding mcm-file for the given molecular type).

&Fixed

- Potential file only. If stated, the potential will be excluded from the inverse procedure (e.g. it will be fixed in potential update/refinement)

&InitZero

- RDF-file only. If the corresponding potential is not provided, initiate it with zero. Default for NB-potentials.

&InitPMF

- RDF-file only. If the corresponding potential is not provided, initiate it with Potential of Mean Force. Default for bond-potentials (both A- and B-).

&Table...&EndTable

- Actual table defining the RDF/potential. The first column specifies distance (Å) or angle (deg), the second column specifies value, which is unitless for RDF and kJ/mol for potential. The table shall be uniformly spaced, and the same grid resolution should be used in all RDFs and potentials of the same kind (NB, B or A) for the whole system

&IncludePotential=IncludeFileName

or

&IncludeRDF=IncludeFileName

- Instead of providing data table in the record, one can import it from an external file <filename>. This feature allows to incorporate easily potentials previously obtained for other systems into the current one.