The RED scheme: Rate-constant estimation from pre-steady state weighted ensemble simulations.

ABSTRACT: We present the Rate from Event Durations (RED) scheme, a new scheme that more efficiently calculates rate constants using the weighted ensemble path sampling strategy. This scheme enables rate-constant estimation from shorter trajectories by incorporating the probability distribution of event durations, or barrier-crossing times, from a simulation. We have applied the RED scheme to weighted ensemble simulations of a variety of rare-event processes that range in complexity: residue-level simulations of protein conformational switching, atomistic simulations of Na⁺/Cl^- association in explicit solvent, and atomistic simulations of protein-protein association in explicit solvent. Rate constants were estimated with up to 50% greater efficiency than the original weighted en

SUBMITTER: DeGrave AJ 

PROVIDER: S-EPMC7972523 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature