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PyRETIS: A well‐done, medium‐sized python library for rare events
Author(s) -
Lervik Anders,
Riccardi Enrico,
van Erp Titus S.
Publication year - 2017
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.24900
Subject(s) - python (programming language) , molecular dynamics , replica , computer science , computational science , rare events , sampling (signal processing) , interface (matter) , statistical physics , computational chemistry , chemistry , physics , parallel computing , mathematics , programming language , art , statistics , filter (signal processing) , bubble , maximum bubble pressure method , visual arts , computer vision
Transition path sampling techniques are becoming common approaches in the study of rare events at the molecular scale. More efficient methods, such as transition interface sampling (TIS) and replica exchange transition interface sampling (RETIS), allow the investigation of rare events, for example, chemical reactions and structural/morphological transitions, in a reasonable computational time. Here, we present PyRETIS, a Python library for performing TIS and RETIS simulations. PyRETIS directs molecular dynamics (MD) simulations in order to sample rare events with unbiased dynamics. PyRETIS is designed to be easily interfaced with any molecular simulation package and in the present release, it has been interfaced with GROMACS and CP2K, for classical and ab initio MD simulations, respectively. © 2017 Wiley Periodicals, Inc.