PyRETIS 2 : An improbability drive for rare events

Bibliographische Detailangaben
Veröffentlicht in:	Journal of computational chemistry. - 1984. - 41(2020), 4 vom: 05. Feb., Seite 370-377
1. Verfasser:	Riccardi, Enrico (VerfasserIn)
Weitere Verfasser:	Lervik, Anders, Roet, Sander, Aarøen, Ola, van Erp, Titus S
Format:	Online-Aufsatz
Sprache:	English
Veröffentlicht:	2020
Zugriff auf das übergeordnete Werk:	Journal of computational chemistry
Schlagworte:	Journal Article Research Support, Non-U.S. Gov't PyRETIS kinetics path sampling python rare event

Beschreibung
Zusammenfassung:	© 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc. The algorithmic development in the field of path sampling has made tremendous progress in recent years. Although the original transition path sampling method was mostly used as a qualitative tool to sample reaction paths, the more recent family of interface-based path sampling methods has paved the way for more quantitative rate calculation studies. Of the exact methods, the replica exchange transition interface sampling (RETIS) method is the most efficient, but rather difficult to implement. This has been the main motivation to develop the open-source Python-based computer library PyRETIS that was released in 2017. PyRETIS is designed to be easily interfaced with any molecular dynamics (MD) package using either classical or ab initio MD. In this study, we report on the principles and the software enhancements that are now included in PyRETIS 2, as well as the recent developments on the user interface, improvements of the efficiency via the implementation of new shooting moves, easier initialization procedures, analysis methods, and supported interfaced software. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc
Beschreibung:	Date Completed 17.08.2020 Date Revised 17.08.2020 published: Print-Electronic Citation Status PubMed-not-MEDLINE
ISSN:	1096-987X
DOI:	10.1002/jcc.26112