Reference

Quick reference

Useful commands

# Activate environment
conda activate md-openmm

# Launch JupyterLab
jupyter lab

Suggested course structure

• docs/episodes/ Carpentries episodes
• docs/data/ sample data
• docs/figures/ figures

Instructor guide

• Check that OpenMM and dependencies work in the classroom.
• Prepare a minimal set of practice data.
• Validate that the notebooks run on GPU and CPU.

Materials

• Example notebooks in docs/episodes/.
• Figures in docs/figures/.

Notes

• Use reproducible seeds when the exercise allows it.
• Save simulation parameters alongside the results.

Link check

python scripts/check_links.py

Generate a DCD trajectory

To create a short DCD with OpenMM:

python scripts/generate_example_dcd.py

This generates alanine-dipeptide.dcd.

Repository technical documentation

For maintenance details and technical documentation, see the README on GitHub:

• README.md on GitHub