RDF Analysis

The RDF Analysis tool computes the radial distribution function g(r) between two groups of atoms along a trajectory, together with the running coordination number N(r): the average number of atoms of group B within a distance r of an atom of group A. Choosing the same group for A and B gives a self-RDF, such as the O–O function of water.

g(r) is normalized by the density of the periodic box, so the trajectory must contain its periodic cell (for example a simulation of a solvated system). If the object has no cell, the tool asks for one (see Reimaging (Wrapping)).

Defining the groups

The groups come from the Selections and Restraints list of the system. Select the atoms in the 3D view (for example, all water oxygens) and use Selection > Send to Selection List; the selection then appears in the Group A and Group B lists. The entry (all atoms) is always available.

Running the analysis

Open Main Menu > Analysis > RDF Analysis (g(r)) (Figure 1):

• System / Object: the trajectory.

• Group A / Group B: the two groups of atoms.

• r max (Å): the largest distance of the histogram (default: 15 Å). Keep it below half of the shortest box length: beyond that point g(r) is no longer complete and decreases artificially.

• Bin width (Å): the width of the histogram bins (default: 0.1 Å).

• Frames from / to and Step Size: the frame range and interval.

• Plot the result: plots g(r) (solid line, left axis) and N(r) (dashed line, right axis), as in Figure 2. The plot can be exported as PNG.

The values of r, g(r) and N(r) are also listed in a text window. Do not run Align Trajectory on a periodic system before computing an RDF: the alignment rotates the whole box and the periodic images no longer match, which produces spurious short distances.