OpenFF ran a series of online workshops in February–April this year. Since then, we have updated materials to take account of issues encountered during the workshops and uploaded re-recordings of all three sessions to YouTube. If you’re interested in understanding the SMIRNOFF force field format, open source protein preparation workflows, or learning about some fun new features and capabilities of the OpenFF ecosystem, take a look!

If you’d like to follow along, each Jupyter notebook worked through in these workshops are available on Google Colab without installing anything on your computer, but we recommend downloading the zipped materials files and installing the software with the included Conda environment to run the workshop locally.

SMIRNOFF Force Fields and You

SMIRNOFF is an open format for specifying molecular mechanics force fields directly for the chemistry of a target molecule, rather than indirectly through abstractions like atom types. Unlike other force field formats, SMIRNOFF describes not only the parameters of the force field, but also the chemistries to which those parameters should be applied.

This workshop introduces the SMIRNOFF format to familiar MD practitioners and describes how a system can be parametrized from a SMIRNOFF force field for a number of different MD engines. We hope to get both users and developers of molecular mechanics force fields excited about this game changing format.

Materials: https://docs.openforcefield.org/workshops/2024/smirnoff.html#workshop-materials

Protein Preparation in Jupyter

Today, Jupyter notebooks are everything you need to prepare a molecular dynamics simulation. Not only do they provide a unified interface to all the tools needed to prepare and visualize a simulation, they also provide an easy way to record, repeat, and even publish your workflow, including any alterations needed for a particularly stubborn system.

This workshop covers the preparation of a protein system from a structure downloaded from the PDB, entirely in the Jupyter notebook, complete with 3D visualizations at every step of the way. We hope to make it accessible even to new MD practitioners, assuming they have some familiarity with Python.

Materials: https://docs.openforcefield.org/workshops/2024/protein_prep.html#workshop-materials

Things to Make and Do with OpenFF Tools

Today, Jupyter notebooks are everything you need to prepare a molecular dynamics simulation. Not only do they provide a unified interface to all the tools needed to prepare and visualize a simulation, they also provide an easy way to record, repeat, and even publish your workflow, including any alterations needed for a particularly stubborn system.

This workshop covers the preparation of a protein system from a structure downloaded from the PDB, entirely in the Jupyter notebook, complete with 3D visualizations at every step of the way. We hope to make it accessible even to new MD practitioners, assuming they have some familiarity with Python.

Materials: https://docs.openforcefield.org/workshops/2024/vignettes.html#workshop-materials