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      A Suite of Tutorials for the WESTPA Rare-Events Sampling Software [Article v1.0]

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          Abstract

          The weighted ensemble (WE) strategy has been demonstrated to be highly efficient in generating pathways and rate constants for rare events such as protein folding and protein binding using atomistic molecular dynamics simulations. Here we present five tutorials instructing users in the best practices for preparing, carrying out, and analyzing WE simulations for various applications using the WESTPA software. Users are expected to already have significant experience with running standard molecular dynamics simulations using the underlying dynamics engine of interest (e.g. Amber, Gromacs, OpenMM). The tutorials range from a molecular association process in explicit solvent to more complex processes such as host-guest association, peptide conformational sampling, and protein folding.

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          Author and article information

          Journal
          101736625
          48120
          Living J Comput Mol Sci
          Living J Comput Mol Sci
          Living journal of computational molecular science
          2575-6524
          14 April 2020
          4 October 2019
          2019
          11 May 2020
          : 1
          : 2
          : 10607
          Affiliations
          [1 ]Department of Chemistry, University of Pittsburgh, Pittsburgh, PA;
          [2 ]Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR;
          [3 ]Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI;
          [4 ]Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA; currently unaffiliated;
          [5 ]Current address: Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA;
          [6 ]Current address: Department of Chemistry, Missouri Valley College, Marshall, MO;
          [7 ]Department of Chemistry, Drake University, Des Moines, IA
          Author notes
          [*]

          These authors contributed equally to this work

          [7]

          Author Contributions

          AT Bogetti, B Mostofian, A Dickson, AJ Pratt, AS Saglam, PO Harrison, JL Adelman, M Dudek, PA Torrillo, AJ DeGrave, and U Adhikari developed and wrote the tutorials; the primary author of each tutorial is designated as a co-first author of the overall manuscript and listed in the order in which the tutorials appear in the manuscript. LT Chong and DM Zuckerman provided guidance for tutorial development. AT Bogetti, LT Chong, DM Zuckerman, AJ Pratt, AS Saglam, B Mostofian, and MC Zwier wrote the introductory sections leading up to the tutorials.

          [8]

          Other Contributions

          We thank the many users of the WESTPA software who have provided important feedback for improving our tutorials and documentation over the past several years. We are also grateful to Samuel Lotz (Dickson Lab) for his contributions to the WESTPA-WExplore plugin.

          For correspondence: ltchong@ 123456pitt.edu (LTC); zuckermd@ 123456ohsu.edu (DMZ)
          Article
          PMC7213600 PMC7213600 7213600 nihpa1584279
          10.33011/livecoms.1.2.10607
          7213600
          32395705
          6023cc0d-3a45-4e65-8e4c-26252f4b93c4
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