RDF Analysis Tutorial

Learn how to compute radial distribution functions (RDF) from molecular dynamics trajectories.

Prerequisites

• An MD trajectory file (.extxyz, .traj, .hdf5)
• Loaded trajectory in the CatGo viewer

Step 1: Load a Trajectory

Load your MD trajectory using the file import dialog or drag-and-drop.

Step 2: Configure RDF Parameters

Element Pairs

Select which element pairs to compute RDF for (e.g., O-H, Si-O).

Cutoff Distance

Set the maximum distance for pair counting (typically 8-12 Angstroms).

Number of Bins

Adjust histogram resolution (default: 200 bins).

Step 3: Compute and Visualize

Click "Compute RDF" to generate the plot. The calculation runs across all trajectory frames.

Multi-Frame Averaging

RDF is averaged over selected frames for better statistics.

Step 4: Interpret Results

Peak Positions

First peak = nearest neighbor distance. Subsequent peaks reveal coordination shell structure.

Coordination Numbers

Integrate g(r) to obtain coordination numbers.

Step 5: Export

Save the plot as SVG/PNG or export raw data as CSV.

Related

• RDF Module — API reference
• Trajectories — Loading MD trajectories