This plugin provides a convenient graphical user interface to the measure gofr command in VMD, which calculates the spherical atomic radial distribution function g(r) between the atoms in two selections over a given trajectory or a subset thereof. You have to have a trajectory already loaded and have the option to either view the resulting g(r) and/or the corresponding number integral in MultiPlot windows or write the result of the calculation to a file.
Selections have to be defined (default is empty). Typical radial distribution functions are computed between elements (same or different), but due to the power of VMD's selection language, very sophisticated distribution functions may be computed.
Note, that the normalization of g(r) has little meaning unless you enable processing of the periodic boundary condition and have a fixed set of atoms in the selection. The number integrals are computed directly and thus provide accurate coordination numbers.
You can use the 'Set unit cell dimension' dialog from the 'Utilities' menu to set the simulation cell information for all frames of the current molecule.
The output file created by the save option contains four columns, the value of r, g(r), the number integral over g(r) and the raw histogram averaged over the number of frames.
In case a selection is empty in a frame, an empty histogram is added to the sum over all frames.
For more detailed explanation of radial distribution and pair correlation functions functions, the following text books are recommended.