PyRETIS 3 Conquering rare and slow events without boundaries

PyRETIS 3 : Conquering rare and slow events without boundaries

© 2024 Wiley Periodicals LLC.

Bibliographische Detailangaben
Veröffentlicht in:Journal of computational chemistry. - 1984. - 45(2024), 15 vom: 05. Apr., Seite 1224-1234
1. Verfasser: Vervust, Wouter (VerfasserIn)
Weitere Verfasser: Zhang, Daniel T, Ghysels, An, Roet, Sander, van Erp, Titus S, Riccardi, Enrico
Format: Online-Aufsatz
Sprache:English
Veröffentlicht: 2024
Zugriff auf das übergeordnete Werk:Journal of computational chemistry
Schlagworte:Journal Article PyRETIS Python kinetics path sampling rare event slow event
Beschreibung
Zusammenfassung:© 2024 Wiley Periodicals LLC.
We present and discuss the advancements made in PyRETIS 3, the third instalment of our Python library for an efficient and user-friendly rare event simulation, focused to execute molecular simulations with replica exchange transition interface sampling (RETIS) and its variations. Apart from a general rewiring of the internal code towards a more modular structure, several recently developed sampling strategies have been implemented. These include recently developed Monte Carlo moves to increase path decorrelation and convergence rate, and new ensemble definitions to handle the challenges of long-lived metastable states and transitions with unbounded reactant and product states. Additionally, the post-analysis software PyVisa is now embedded in the main code, allowing fast use of machine-learning algorithms for clustering and visualising collective variables in the simulation data
Beschreibung:Date Revised 18.04.2024
published: Print-Electronic
Citation Status PubMed-not-MEDLINE
ISSN:1096-987X
DOI:10.1002/jcc.27319