A Suite of Tutorials for the WESTPA 2.0 Rare-Events Sampling Software [Article v2.0].

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 two sets of tutorials instructing users in the best practices for preparing, carrying out, and analyzing WE simulations for various applications using the WESTPA software. The first set of more basic tutorials describes a range of simulation types, from a molecular association process in explicit solvent to more complex processes such as host-guest association, peptide conformational sampling, and protein folding. The second set ecompasses six advanced tutorials instructing users in the best practices of using key new features and plugins/extensio

SUBMITTER: Bogetti AT 

PROVIDER: S-EPMC10191340 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature