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 are defined. Each distribution function defined at this stage results 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 CG system.

Input files:

*Molecular type description

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

*CG trajectory

: [XMOL]*.xmol or *.xtc. NB! It is assumed that molecules in the trajectory are kept whole against PBC, which shall be the case if you had molecules whole in the original all-atom trajectory.

*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

Output files:

Reference distribution functions

*.rdf. [RDFnPOT]See format details

Coarse-Grain molecular topology

*.mcm. [MCM]See format details.

Exclusions file

exclusions.dat. [exclusions.dat]See format details.

Run:

rdf.py -i rdf.inp [-np n_cores] [--force]
To run in parallel mode, specify the number of cores n_cores, and to avoid check of atom names consistency use option --force