RDF Analysis (version @VERSION@)

DCD/XTC trajectory input:

PDB/GRO input:

Segment ID of atom 1:

Residue ID of atom 1:

Atom name of atom 1:

Segment ID of atom 2:

Residue ID of atom 2:

Atom name of atom 2:

Number of bins in the histogram:

Starting point (angstroms):

Minimum value of r to calculate RDF for

End point (angstroms):

Maximum value of r to calculate RDF for

What it does

The Radial Distribution Function (RDF), g(r), also called pair distribution function or pair correlation function, can be used to find how density varies as a function of distance from a reference atom.

Input

Trajectory file (DCD).

PDB file.

Segment IDs, residue IDs and names of two atoms to calculate RDF values.

Note that a MDAnalysis 'segment' is a larger organizational unit, for example one protein or all the solvent molecules or simply the whole system.

Other parameters can also be specified: the number of bins in the RDF histogram, and the start and end points for the calculation (i.e. the values of r between which RDF will be calculated).

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Other parameters can also be specified: the number of bins in the RDF histogram, and the start and end points for the calculation (i.e. the values of r between which RDF will be calculated).
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Output

Tab-separated file of raw data of the RDF.

Image (as png) of the RDF plot.