[Folding@home] OpenPathSampling: A Python Framework for Path Sampling Simulations. 1. Basics

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J Chem Theory Comput. 2019 Feb 12;15(2):813-836. doi: 10.1021/acs.jctc.8b00626. Epub 2018 Dec 31. ABSTRACT 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...

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