This workshop source repository contains the build recipe for a docker container derived from the CCPBioSim JupyterHub image. This container adds the necessary software packages and notebook content to form a deployable course container.
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.
- 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.
This training course is deployed on the CCPBioSim website via our cloud infrastructure, however you can deploy on your own machine with docker.
Pull the container from our repository::
docker pull ghcr.io/ccpbiosim/openff-workshop:latest
In our containers we are using the JupyterHub default port 8888, so you should forward this port when deploying locally::
docker run -p 8888:8888 ghcr.io/ccpbiosim/openff-workshop:latest
Workshop Content Authors:
- Danny Cole
- Finlay Clark
Please direct all questions and feedback to Finlay Clark or Danny Cole