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¶
- For more information on running ABFE simulations, see the ABFE documentation
- For details on the
Complex
class, refer to the API reference