Skip to content

Visualizing ABFE Trajectories

This guide explains how to visualize molecular dynamics trajectories from Absolute Binding Free Energy (ABFE) simulations in Deep Origin.

Overview

ABFE simulations generate molecular dynamics trajectories that show how ligands interact with proteins over time. Visualizing these trajectories can provide valuable insights into binding mechanisms, protein-ligand interactions, and conformational changes.

Deep Origin provides tools to easily visualize these trajectories using the show_trajectory method in the ABFE class.

Prerequisites

  • A completed ABFE simulation run
  • Valid ligand ID from your simulation
  • The Deep Origin Python package properly installed and configured

Visualizing Trajectories

Using the show_trajectory Method

The show_trajectory method allows you to visualize either the molecular dynamics (md) phase or the binding phase of an ABFE run.

Before using this method, you'll need to have a properly set up Complex object with completed ABFE calculations. For a complete walkthrough of setting up your environment, creating a Complex object, and running ABFE calculations, please refer to the Getting Started tutorial.

Once you've completed the steps in the tutorial and have run your ABFE calculations, you can return to this guide to visualize the trajectories.

Behind the Scenes

When you call show_trajectory, the following happens: 1. The method retrieves result files for the specified ABFE run 2. It extracts the trajectory files from a ZIP archive (if not already extracted) 3. It generates a 3D visualization using the deeporigin_molstar library 4. The visualization is displayed in your Jupyter notebook

Examples

Visualizing Molecular Dynamics Step

# Show the molecular dynamics trajectory
sim.abfe.show_trajectory(ligand_id="ligand1", step="md")

Visualizing Binding Step

sim.abfe.show_trajectory(ligand_id="ligand1", step="binding")

Troubleshooting

If you encounter issues when visualizing trajectories:

  • Ensure your ABFE run completed successfully
  • Verify that the ligand ID is correct
  • Check that the specified step ("md" or "binding") is available
  • Ensure you have sufficient disk space for extracting trajectory files

Additional Resources