OpenPathSampling

A Python library to facilitate path sampling algorithms.

OpenPathSampling (OPS) makes it easy to perform many variants of transition path sampling (TPS) and transition interface sampling (TIS), as well as other useful calculations for rare events, such as committor analysis and flux calculations. In addition, it is a powerful library to build new path sampling methods.

OPS is independent of the underlying molecular dynamics engine, and currently has support for OpenMM and Gromacs, as well as an internal engine suitable for 2D toy models.

To learn more about what OPS can do, look at our examples. If you want to jump right in, take a look at how easy it is to install!

OPS is an open-source project, distributed under the MIT license. Join us in the development process on GitHub, and follow @pathsampling on Twitter for updates!

Note

Documentation is still in progress. Please see Getting Help for how to contact us with questions.

To see the most recent updates to the code, see the release notes page on GitHub.

Citing

OPS was described in a pair of papers published in JCTC:

1. David W.H. Swenson, Jan-Hendrik Prinz, Frank Noé, John D. Chodera, and Peter G. Bolhuis. “OpenPathSampling: A flexible, open framework for path sampling simulations. 1. Basics.” J. Chem. Theory Comput. 15, 813 (2019). https://doi.org/10.1021/acs.jctc.8b00626

2. David W.H. Swenson, Jan-Hendrik Prinz, Frank Noé, John D. Chodera, and Peter G. Bolhuis. “OpenPathSampling: A flexible, open framework for path sampling simulations. 2. Building and Customizing Path Ensembles and Sample Schemes.” J. Chem. Theory Comput. 15, 837 (2019). https://doi.org/10.1021/acs.jctc.8b00627

Both citations: openpathsampling.bib (citation keys ops1 and ops2).

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For Users

• Installation
  • Installing OpenPathSampling
  • Integration with other packages
  • Testing your installation
• Examples
  • Tutorial
  • Introductory Examples
  • Advanced Examples
  • Special Topics
  • Miscellaneous Examples
• User Guide Topics
  • OpenPathSampling terminology
  • Preparing for path sampling
  • Setting up sample sets
  • Output during simulations
  • Data objects
  • Creating collective variables
  • Ensembles apply to trajectories, not frames
  • Common setups
  • Which network should I use?
  • Transitions and Networks
  • TIS Analysis
  • Advanced Uses of OPS Ensembles
  • How I use OpenPathSampling
• Videos
  • Introduction to Path Sampling
  • Developing for OpenPathSampling
• Command Line Interface
  • Workflow with the CLI
  • The Compile Command
  • Expression Evaluation
• The OPS Ecosystem
• Frequently Asked Questions
• Getting Help

For Developers

• Overviews for Developers
  • General Advice for Developers
  • Installing for developers and beta-testers
  • Code Structure
  • Path Simulators
  • Hooks in Path Simulators
  • Engines
  • PathMovers and MoveStrategies
  • Collective Variables
  • Storage
• OpenPathSampling API
  • Data Objects
  • Collective Variables
  • Volumes
  • Ensembles
  • PathMovers
  • Engines
  • Storage Functions
  • PathSimulators
  • ShootingPointSelectors
  • Snapshot Modifiers
  • MoveStrategy
  • Interface Sets
  • Networks and Transitions
  • netCDF+ package
  • Numerics
  • TreeMixin
  • Analysis Tools
  • TIS Analysis Tools

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License

OpenPathSampling is licensed under the MIT license.