Computing transition path theory quantities with trajectory stratification

Bodhi P. Vani, Jonathan Weare, Aaron R. Dinner

Research output: Contribution to journalArticlepeer-review

Abstract

Transition path theory computes statistics from ensembles of reactive trajectories. A common strategy for sampling reactive trajectories is to control the branching and pruning of trajectories so as to enhance the sampling of low probability segments. However, it can be challenging to apply transition path theory to data from such methods because determining whether configurations and trajectory segments are part of reactive trajectories requires looking backward and forward in time. Here, we show how this issue can be overcome efficiently by introducing simple data structures. We illustrate the approach in the context of nonequilibrium umbrella sampling, but the strategy is general and can be used to obtain transition path theory statistics from other methods that sample segments of unbiased trajectories.

Original languageEnglish (US)
Article number034106
JournalJournal of Chemical Physics
Volume157
Issue number3
DOIs
StatePublished - Jul 21 2022

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

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