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Sampling free energy surfaces as slices by combining umbrella sampling and metadynamics
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Awasthi, Shalini, Kapil, Venkat and Nair, Nisanth N. (2016) Sampling free energy surfaces as slices by combining umbrella sampling and metadynamics. Journal of Computational Chemistry, 37 (16). pp. 1413-1424. doi:10.1002/jcc.24349 ISSN 0192-8651.
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Official URL: http://dx.doi.org/10.1002/jcc.24349
Abstract
Metadynamics (MTD) is a very powerful technique to sample high‐dimensional free energy landscapes, and due to its self‐guiding property, the method has been successful in studying complex reactions and conformational changes. MTD sampling is based on filling the free energy basins by biasing potentials and thus for cases with flat, broad, and unbound free energy wells, the computational time to sample them becomes very large. To alleviate this problem, we combine the standard Umbrella Sampling (US) technique with MTD to sample orthogonal collective variables (CVs) in a simultaneous way. Within this scheme, we construct the equilibrium distribution of CVs from biased distributions obtained from independent MTD simulations with umbrella potentials. Reweighting is carried out by a procedure that combines US reweighting and Tiwary–Parrinello MTD reweighting within the Weighted Histogram Analysis Method (WHAM). The approach is ideal for a controlled sampling of a CV in a MTD simulation, making it computationally efficient in sampling flat, broad, and unbound free energy surfaces. This technique also allows for a distributed sampling of a high‐dimensional free energy surface, further increasing the computational efficiency in sampling. We demonstrate the application of this technique in sampling high‐dimensional surface for various chemical reactions using ab initio and QM/MM hybrid molecular dynamics simulations. Further, to carry out MTD bias reweighting for computing forward reaction barriers in ab initio or QM/MM simulations, we propose a computationally affordable approach that does not require recrossing trajectories.
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): | Surface chemistry -- Statistics, Surface energy | |||||||||
Journal or Publication Title: | Journal of Computational Chemistry | |||||||||
Publisher: | John Wiley & Sons, Inc. | |||||||||
ISSN: | 0192-8651 | |||||||||
Official Date: | 15 June 2016 | |||||||||
Dates: |
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Volume: | 37 | |||||||||
Number: | 16 | |||||||||
Page Range: | pp. 1413-1424 | |||||||||
DOI: | 10.1002/jcc.24349 | |||||||||
Status: | Peer Reviewed | |||||||||
Publication Status: | Published | |||||||||
Reuse Statement (publisher, data, author rights): | "This is the peer reviewed version of the following article: Awasthi, Shalini, Kapil, Venkat and Nair, Nisanth N. (2016) Sampling free energy surfaces as slices by combining umbrella sampling and metadynamics. Journal of Computational Chemistry, 37 (16). pp. 1413-1424., which has been published in final form at doi:10.1002/jcc.24349. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions." | |||||||||
Access rights to Published version: | Restricted or Subscription Access | |||||||||
Date of first compliant deposit: | 3 September 2018 | |||||||||
Date of first compliant Open Access: | 3 September 2018 | |||||||||
RIOXX Funder/Project Grant: |
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