RMSD & RMSF Tutorial

Learn how to compute root-mean-square deviation (RMSD) and root-mean-square fluctuation (RMSF) from molecular dynamics trajectories.

Prerequisites

• An MD trajectory loaded in CatGo

Step 1: Open MD Analysis

Navigate to the MD Analysis pane from the sidebar.

Step 2: Compute RMSD

Reference Frame

Select the reference frame (default: first frame) for RMSD calculation.

Atom Selection

Choose which atoms to include (all atoms, backbone only, or custom selection).

Results

The RMSD time series shows structural drift from the reference. Equilibrated systems show a plateau.

Step 3: Compute RMSF

Per-Atom Fluctuations

RMSF shows the average displacement of each atom over the trajectory.

Visualization

RMSF values can be mapped to atom colors or sizes in the 3D viewer.

Step 4: Export

Export time series data or per-atom RMSF values.

Related

• Dynamics Module — API reference
• Trajectory Playback — Loading trajectories