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

• DOI: 10.33011/livecoms.1.2.10607
• Publication Date: 2019-10-02T15:12:05Z
• Authors: Anthony T. Bogetti; Barmak Mostofian; Alex Dickson; AJ Pratt; Ali S. Saglam; Paige O. Harrison; Joshua LL. Adelman; Max Dudek; Paul A. Torrillo; Alex J. DeGrave; Upendra Adhikari; Matthew C. Zwier; Daniel M. Zuckerman; Lillian T. Chong
• Keywords: Folding (DSP implementation); Software suite

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 binding using atomistic molecular dynamics simulations. Here we present five tutorials instructing users the best practices preparing, carrying out, analyzing WE simulations various applications WESTPA software. Users are expected already have significant experience with running standard underlying engine of interest (e.g. Amber, GROMACS, OpenMM). range from a association process explicit solvent more complex processes host-guest association, peptide conformational sampling, folding.