Committor Analysis in OpenPathSampling

Software Technical Information

The information in this section describes OpenPathSampling as a whole. Information specific to the additions in this module are in subsequent sections.

Language
Python (2.7)
Documentation Tool
Sphinx, numpydoc format (ReST)
Application Documentation
http://openpathsampling.org
Relevant Training Material
http://openpathsampling.org/latest/examples/
Licence
LGPL, v. 2.1 or later

Authors: David W.H. Swenson

This module adds a simulator to perform committor analysis in OpenPathSampling, given a set of initial points to shoot from.

Purpose of Module

The committor for a given configuration (in the context of some transition A\to B) is defined as p_B(x), the probability that a trajectory beginning at configuration x will reach state B before state A. The isosurfaces of the committor are a good definition of the reaction coordinate (the probability of ending in the product state is certainly a measure of the progress of the reaction). The transition state will have an equal chance of going to either state, so configurations with a committor of approximately 50% are said to make up the “transition state ensemble.” As a result, a committor simulation is essential both for the definition of the reaction coordinate and for the identification of a proposed transition state. This module provides a straightforward way of calculating the committor for a given set of initial conditions.

In addition to calculating the committor, this module can be used to generate more physical transition trajetories from unphysical ones. A trajectory that connects the two states and has the same initial configuration could be a good candidate for an initial path sampling trajectory. The only unphysical aspect of such a trajectory is the sudden kink in velocities, which usually be removed after a short equilibration with path sampling.

The implementation in this module includes:

  • SnapshotModifier abstract class to change a snapshot, along with concrete subclasses NoModification (used in testing) and RandomVelocities (used for committor analysis). This same class of object will be reused for two-way shooting.
  • A CommittorSimulation subclass of PathSimulator to run the committor simulation.
  • A generic TransformedDict object which acts as a dictionary, but applies an arbitrary key-altering function before accessing the keys.
  • SnapshotByCoordinateDict, a subclass of TransformedDict, which uses the coordinates of a snapshot as the internal keys. Thus multiple snapshots with the same coordinates can map to the same values, regardless of their velocities.
  • ShootingPointAnalysis, a subclass of SnapshotByCoordinateDict, which performs the analysis of shooting points. This includes calculating the committor and making 1D and 2D histograms of the committor (mapped with arbitrary axes).

Background Information

This module builds on OpenPathSampling, a Python package for path sampling simulations. To learn more about OpenPathSampling, you might be interested in reading:

Testing

Tests in OpenPathSampling use the nose package.

This module has been included in the OpenPathSampling core. Its tests can be run by setting up a developer install of OpenPathSampling and running the command nosetests from the root directory of the repository.

Examples