This is a simple radial distribution function (RDF) calculation for use with GROMACS output. GROMACS already includes a utility for calculating an RDF, so this is probably just useful as an example. It uses libgmxcpp which reads in all frames at the beginning so the calculation can be run in parallel.
libgmxcpp is required.
git clone firstname.lastname@example.org:wesbarnett/rdf.git cd rdf make
To run, do the following:
An example configuration file is found in the repository. It should have the following, in this order:
- Name of xtc file to read in
- Name of index file to read in
- Name of output file
- Name of first group in rdf calculation
- Name of second group in rdf calculation (can be the same as the first)
- Exclusion distance (so that atoms on the same molecule won't be counted)
- Bin width
- Location of last bin
Again, see the example in conf.in.
Just for fun, here is an example of a water-water (OW-OW) RDF for TIP4PEW using output from this program: