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

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.

SUBMITTER: Bogetti AT

PROVIDER: S-EPMC7213600 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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

Bogetti Anthony T AT Mostofian Barmak B Dickson Alex A Pratt A J AJ Saglam Ali S AS Harrison Page O PO Adelman Joshua L JL Dudek Max M Torrillo Paul A PA DeGrave Alex J AJ Adhikari Upendra U Zwier Matthew C MC Zuckerman Daniel M DM Chong Lillian T LT

Living journal of computational molecular science 20191004 2

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 molecula ...[more]

PMID: 32395705

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