Some illustrative examples created to support the lectures "Studying rare events in molecular dynamics simulations: from free energies to mechanistic insights" at the 2021 Han-sur-Lesse Winterschool in Theoretical Chemistry and Spectroscopy.

All examples are simulations conducted with PLUMED + CP2K/LAMMPS. Input files necessary to reproduce them are provided. Useful outputs for instant analysis are readily available. The most important points of interest and analysis are contained within the analysis.ipynb Jupyter notebooks in each directory.

Usually, the notebooks should render directly inside the GitHub web interface, but its performance seems flaky at best. So, alternatively, you can use the nbviewer service.

The lecture slides associated with these notebooks are included in PDF format.