Hydrogen Bond Detection Tutorial

Learn how to detect and analyze hydrogen bonds across MD trajectory frames.

Prerequisites

• An MD trajectory with hydrogen atoms

Step 1: Configure Detection Criteria

Geometric Criteria

• D-A distance cutoff: Maximum donor-acceptor distance (default: 3.5 A)
• D-H-A angle cutoff: Minimum angle (default: 120 degrees)

Donor/Acceptor Elements

Select which elements act as donors and acceptors.

Step 2: Run Detection

Hydrogen bonds are detected frame-by-frame across the trajectory.

Step 3: Analyze Results

H-Bond Count Time Series

Track how the number of hydrogen bonds evolves over time.

H-Bond Lifetime

Compute autocorrelation functions to determine H-bond lifetimes.

Donor-Acceptor Pairs

Identify the most common H-bond pairs.

Step 4: Visualize

H-bonds can be overlaid on the 3D structure view as dashed lines.

Related

• H-Bonds Module — API reference