[Folding@home] OpenPathSampling: A Python Framework for Path Sampling Simulations. 2. Building and Customizing Path Ense

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J Chem Theory Comput. 2019 Feb 12;15(2):837-856. doi: 10.1021/acs.jctc.8b00627. Epub 2018 Dec 31. ABSTRACT The OpenPathSampling (OPS) package provides an easy-to-use framework to apply transition path sampling methodologies to complex molecular systems with a minimum of effort. Yet, the extensibility of OPS allows for the exploration of new path sampling algorithms by building on a variety of basic operations. In a companion paper [ Swenson et al. J. Chem. Theory Comput. 2018 , 10.1021/acs.jctc.8b00626 ] we introduced the basic concepts and the structure of the OPS package, and how it can be employed to perform standard transition path sampling and (replica exchange) transition interface sampling. In this paper, we elaborate on two theoretical developments that went into the design of OPS. The first development...

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