RDF

The RDF analysis computes the radial distribution function between two groups. It is useful for analyzing local packing, solvation structure, and characteristic interaction distances.

Adding the plot

1. Open Path Analyzer.
2. Choose RDF in Observable.
3. Choose a Path.
4. Define Group A and Group B.
5. Set the Maximum radius and Bin width.
6. Click Add RDF.

Inputs

• Two atom-containing selections are required.
• Maximum radius defines how far out the distribution is sampled.
• Bin width controls the radial resolution.

View

• Radial distribution function: a one-dimensional curve of density versus distance.

Key equations

At the simplest level, the RDF counts how many sampled pairs fall into a shell around distance \(r\):

\[ g(r)\propto \frac{n(r)}{\Delta V(r)},\qquad \Delta V(r)\approx 4\pi r^2\Delta r \]

When periodic cell information is available, Path Analyzer can normalize this count against the expected ideal-gas occupancy of the shell and report a properly scaled \(g(r)\). Without that information, it falls back to an RDF-like curve in arbitrary units.

Note

• When valid unit-cell information is available, Path Analyzer can report a properly normalized g(r).
• When periodic normalization is not possible, the app falls back to an unnormalized RDF-style curve in arbitrary units.
• RDF cards are not frame-linked, because they summarize the path globally.

Tip

• Choose a bin width that is fine enough to resolve peaks but not so fine that the curve becomes too noisy.
• Use chemically meaningful groups, for example solute-solvent, ligand-pocket, or residue-residue subsets.