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Exploring high-dimensional free energy landscapes of chemical reactions

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Awasthi, Shalini and Nair, Nisanth N. (2019) Exploring high-dimensional free energy landscapes of chemical reactions. Wiley Interdisciplinary Reviews : Computational Molecular Science, 9 (3). e1398. doi:10.1002/wcms.1398

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Official URL: http://dx.doi.org/10.1002/wcms.1398

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Abstract

Molecular dynamics (MD) techniques are widely used in computing free energy changes for conformational transitions and chemical reactions, mainly in condensed matter systems. Most of the MD‐based approaches employ biased sampling of a priori selected coarse‐grained coordinates or collective variables (CVs) and thereby accelerate otherwise infrequent transitions from one free energy basin to the other. A quick convergence in free energy estimations can be achieved by enhanced sampling of large number of CVs. Conventional enhanced sampling approaches become exponentially slower with increasing dimensionality of the CV space, and thus they turn out to be highly inefficient in sampling high‐dimensional free energy landscapes. Here, we focus on some of the novel methods that are designed to overcome this limitation. In particular, we discuss four methods: bias‐exchange metadynamics, parallel‐bias metadynamics, adiabatic free energy dynamics/temperature‐accelerated MD, and temperature‐accelerated sliced sampling. The basic idea behind these techniques is presented and applications using these techniques are illustrated. Advantages and disadvantages of these techniques are also delineated.

Item Type: Journal Article
Subjects: Q Science > QD Chemistry
Divisions: Faculty of Science > WMG (Formerly the Warwick Manufacturing Group)
Library of Congress Subject Headings (LCSH): Chemical reactions, Molecular dynamics, Condensed matter
Journal or Publication Title: Wiley Interdisciplinary Reviews : Computational Molecular Science
Publisher: Wiley-Blackwell Publishing Ltd.
ISSN: 1759-0876
Official Date: May 2019
Dates:
DateEvent
May 2019Published
16 November 2018Available
5 October 2018Accepted
Volume: 9
Number: 3
Article Number: e1398
DOI: 10.1002/wcms.1398
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Restricted or Subscription Access
RIOXX Funder/Project Grant:
Project/Grant IDRIOXX Funder NameFunder ID
UNSPECIFIEDDepartment of Biotechnology , Ministry of Science and Technologyhttp://dx.doi.org/10.13039/501100001407

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