Examples

This page provides a series of examples, tutorials and recipes to help you get started with openpathsampling.

Each subsection of the pages linked below is a notebook. To open these notebooks in a “live” session and execute the documentation interactively, open them using jupyter notebook NOTEBOOK_NAME.ipynb.

If you installed openpathsampling from source, you can find these in the examples directory within the root openpathsampling directory. You cn also find them in our GitHub repository.

Note

It’s a lot more fun to run these examples live than to just read them here!

Introductory Examples

These examples give the entire process of a path sampling simulation: going from an initial frame to a set of initial trajectories, performing the path sampling, and the analyzing the results.

We recommend beginning with those two examples: they cover most of the essential points of using OPS. Additionally, there’s a tutorial version of the alanine dipeptide TPS example, if you prefer a version where you have to add the missing pieces to make it run. We also have several other examples which show how to use these approaches for specific cases. Here are several of those:

Note that some of those build off of the earlier examples. If working through the example notebooks yourself, each notebook in a sequence is numbered so you know the order to run them.

Advanced Examples

The advanced examples demonstrate some of the more specialized uses of OPS.

Special Topics

In order to illustrate several features of the code, we have also developed some “special topics” examples. These usually require that you have already run one of the introductory examples, but demonstrate some optional behavior you might find interesting.

In addition, there are a set of examples that are hosted outside the core OPS repository. These are the OPS additional examples, primarily developed as part of E-CAM, a European Union Horizon 2020 project. Those examples are available at https://gitlab.e-cam2020.eu/dwhswenson/ops_additional_examples.

Miscellaneous Examples

The examples above provide most of the tools that you might need. However, to document various other tricks and workflows, we have a page of miscellaneous examples.


Let us know if you would like to contribute other example notebooks, or have any suggestions for how these can be improved.