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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 ISSN 1759-0876.
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Official URL: http://dx.doi.org/10.1002/wcms.1398
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 | ||||||||
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| Subjects: | Q Science > QD Chemistry | ||||||||
| Divisions: | Faculty of Science, Engineering and Medicine > Engineering > 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: |
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| 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 | ||||||||
| Date of first compliant deposit: | 30 November 2018 | ||||||||
| Date of first compliant Open Access: | 16 November 2019 | ||||||||
| RIOXX Funder/Project Grant: |
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