These tutorials were delivered at the 2025 CCPBioSim training week, but are suitable for self-guided learning.
Presenters:
- Danny Cole
- Finlay Clark
We recommend you view the materials in the following order:
- Talk: Intro to OpenFF
- Notebook: Parameterising small molecules with OpenFF
- Notebook: Parameterisation, molecular dynamics, and basic trajectory analysis for a protein-ligand complex
Answers to most exercises are given in the notebooks_with_solutions directory.
To use these notebooks on your local machine, we recommend using mamba to create an environment from the provided YAML file:
$ mamba env create --file environment.yaml
$ ...
$ mamba activate openff-env- Main OpenFF docs
- See "Projects" on the left for package-specific documentation
- Ecosystem-wide examples
- SMIRNOFF specification
- Discussions - for general usage questions
Most of the material for the notebook Parameterising small molecules with OpenFF was adapted from the 2023 CCPBioSim Workshop Open Force Field Sessions created by Matt Thompson and Jeff Wagner.
Most of the material for the notebook Parameterisation, molecular dynamics, and basic trajectory analysis for a protein-ligand complex was adapted from the OpenFF toolkit showcase and the ProLIF Ligand-protein MD tutorial.