rdf.py: Reference Distribution Functions calculation

This section describes calculation of the structural distribution functions (DF), which will be used as a reference for the effective potentials calculation during the inverse process. Note, that after the previous stage (cgtraj), the generated CG trajectory does not have any information about chemical CG types or bonding, and this information is provided at this stage when CG types and their bonding is defined. Each distribution function will result in an individual interaction potential, therefore definition of groups of beads, which belong to a certain DF, is equivalent to definition of specific interactions in the system.

Input files:

*Molecular type description

for each type present in the system:
[MMOL]*.mmol or [MCM]*.mcm.

*CG trajectory

: [XMOL]*.xmol.

*Main input

defining RDF calculation parameters, input trajectory, CG-atom/bead types and the list of RDFs to calculate (and beads included in each specific RDF): [rdf.inp]rdf.inp
NB! The [rdf.inp] new input format was introduced in MagiC 2.0, however, the old format of v.1.x is still supported and detected automatically.

Output files:

Reference distribution functions

: *.rdf. [RDFnPOT]See format details

Coarse-Grain topology

*.mcm. [MCM]See format details.

Run:

rdf.py -i rdf.inp