PyRETIS 3: Conquering rare and slow events without boundaries.

Autor: Vervust W; IBiTech-BioMMedA Group, Ghent University, Ghent, Belgium., Zhang DT; Department of Chemistry, Norwegian University of Science and Technology, Trondheim, Norway., Ghysels A; IBiTech-BioMMedA Group, Ghent University, Ghent, Belgium., Roet S; Department of Chemistry, Utrecht University, Utrecht, The Netherlands., van Erp TS; Department of Chemistry, Norwegian University of Science and Technology, Trondheim, Norway., Riccardi E; Department of Energy Resources, University of Stavanger, Stavanger, Norway.
Jazyk: angličtina
Zdroj: Journal of computational chemistry [J Comput Chem] 2024 Jun 05; Vol. 45 (15), pp. 1224-1234. Date of Electronic Publication: 2024 Feb 12.
DOI: 10.1002/jcc.27319
Abstrakt: 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.
(© 2024 Wiley Periodicals LLC.)
Databáze: MEDLINE
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