Examples

This page assembles examples drawn from throughout the OpenFF stack. Each example is provided in the form of a notebook; that is, as annotated code blocks alongside their output. You can download the corresponding notebook file and run it yourself either locally or in Google Colab with the links at the top of each page.

Tutorials

Tutorials describing key workflows from start to finish, with detailed explanations of what’s going on.

Protein-ligand-water systems with Interchange
openff-interchange
Solvate and equilibrate a ligand in a box of water
openff-interchange
Toolkit Showcase: Prepare and run a protein-ligand simulation
openff-toolkit
Visualizations in the OpenFF Toolkit
openff-toolkit

Parametrization and Evaluation

Quick examples describing use of OpenFF tools for system prep, parametrization, energy evaluation, and simulation.

Simulate an Interchange with OpenMM
openff-interchange
Generate and parameterize multi-component systems
openff-interchange
Simulate an Interchange with LAMMPS
openff-interchange
Compute conformer energies for a small molecule with Interchange
openff-interchange
Mixture simulation with Sage: Ethanol and cyclohexane
openff-toolkit
Compute conformer energies for a small molecule
openff-toolkit
Using OpenFF force fields in Amber and GROMACS
openff-toolkit
Prepare a SMIRNOFF ligand with openmmforcefields and Interchange
experimentalopenff-interchange

Combining Force Fields

Examples combining OpenFF and SMIRNOFF force fields with force fields from other projects.

Mixing Sage and Amber force fields: BRD4 benchmark
openff-toolkit
Load a system from OpenMM into Interchange
experimentalopenff-interchange
Mixing Sage and Amber: BRD4 benchmark with ParmEd
openff-toolkit
Mixing Sage and Amber: Full parametrization with OpenMM Force Fields
openff-toolkit
Mixing Sage and Amber: Sage ligands in an existing Amber system with ParmEd
openff-toolkit

Force Field Development

Modifying, tweaking, manipulating, inspecting, and re-fitting force fields.

Vectorized force field representations
openff-interchange
Virtual Sites Showcase
openff-toolkit
Modifying a SMIRNOFF force field
openff-toolkit
Inspect parameters assigned to specific molecules
openff-toolkit

Uncategorized

Notebooks that don’t fit in to the above categories.

Training a Graph Neural Network with NAGL
openff-nagl
Training a Graph Neural Network with NAGL with multiple objectives
openff-nagl
Prepare a NAGL dataset for training
openff-nagl
Building a variety of different virtual sites
openff-interchange
Host-guest systems
openff-interchange
Using QCArchive with the OpenFF Toolkit
openff-toolkit
Methods for Topology solvation
experimentalopenff-interchange

Running examples locally

Each example (links above) provides a “Download notebook” link, which downloads a compressed .TGZ archive including the notebook, all the files needed to run it, a Conda environment specification YAML file, and a script called run_notebook.sh. Extracting the entire file and executing this script will download all the software needed to run the notebook into a virtual environment and then run the notebook:

./run_notebook.sh

For more information, see the comments in the script itself. If you have a Mamba installation already (see Installation), you can prepare the environment by hand:

mamba env create --file environment.yaml --name openff-examples
mamba activate openff-examples
jupyter lab *.ipynb