OpenPathSampling: A Python Framework for Path Sampling Simulations. 1. Basics

• Published in: Journal of chemical theory and computation Vol. 15; no. 2; pp. 813 - 836
• Main Authors: Swenson, David W. H, Prinz, Jan-Hendrik, Noe, Frank, Chodera, John D, Bolhuis, Peter G
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 12.02.2019
• Subjects: Algorithms; Complex systems; Complexity; Computer simulation; Importance sampling; Molecular dynamics; Simulation
• ISSN: 1549-9618; 1549-9626; 1549-9626
• DOI: 10.1021/acs.jctc.8b00626

Transition path sampling techniques allow molecular dynamics simulations of complex systems to focus on rare dynamical events, providing insight into mechanisms and the ability to calculate rates inaccessible by ordinary dynamics simulations. While path sampling algorithms are conceptually as simple as importance sampling Monte Carlo, the technical complexity of their implementation has kept these techniques out of reach of the broad community. Here, we introduce an easy-to-use Python framework called OpenPathSampling (OPS) that facilitates path sampling for (bio)­molecular systems with minimal effort and yet is still extensible. Interfaces to OpenMM and an internal dynamics engine for simple models are provided in the initial release, but new molecular simulation packages can easily be added. Multiple ready-to-use transition path sampling methodologies are implemented, including standard transition path sampling (TPS) between reactant and product states and transition interface sampling (TIS) and its replica exchange variant (RETIS), as well as recent multistate and multiset extensions of transition interface sampling (MSTIS, MISTIS). In addition, tools are provided to facilitate the implementation of new path sampling schemes built on basic path sampling components. In this paper, we give an overview of the design of this framework and illustrate the simplicity of applying the available path sampling algorithms to a variety of benchmark problems.