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 OPS from source, you can find these in the examples directory within the root openpathsampling directory. You can 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!

Tutorial

One of the best ways to get familiar with OPS is our tutorial, which has been used in several workshops and classrooms over the years. The main part of the tutorial (notebooks numbered 1-3) is essentially the same as the alanine dipeptide TPS example, and usually takes no more than 90 minutes to complete. It can be downloaded at the link below or directly launched in Binder. Read the README file for details on using the tutorial.

• https://github.com/openpathsampling/ops_tutorial

There’s also a YouTube video of the tutorial as it was presented at a workshop in 2017.

Introductory Examples

The next 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.

• Flexible Length TPS on Alanine Dipeptide
  • Obtaining an equilibrated initial trajectory
  • Running the production TPS simulation
  • Analyzing the flexible path length simulation
• Multiple State TIS on a Toy Model
  • Obtaining the first trajectories for a Toy Model
  • Running an MSTIS simulation
  • Analyzing the MSTIS simulation

We recommend beginning with those two examples: they cover most of the essential points of using OPS. We also have several other examples which show how to use these approaches for specific cases. Here are several of those:

• Fixed Length TPS on Alanine Dipeptide
• Multiple state TIS on Alanine Dipeptide
• Multiple Interface Set TIS on a Toy Model
• Single Replica TIS on a Toy Model

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.

• Advanced TPS Analysis on Alanine Dipeptide
• Custom Move Strategy and Path Mover

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.

• OpenPathSampling Storage
• Continuing a Path Sampling Simulation
• Splitting Files
• Customizing Visualizations
• Understanding Move Schemes and Strategies

More examples can be found in the OPS additional examples repository. Live versions of those examples are also available through binder.

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.

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