Banushkina, PV and Krivov, SV (2015) Fep1d: A Script for the Analysis of Reaction Coordinates. Journal of Computational Chemistry, 36 (12). pp. 878-882. ISSN 0192-8651
Abstract
The dynamics of complex systems with many degrees of freedom can be analyzed by projecting it onto one or few coordinates (collective variables). The dynamics is often described then as diffusion on a free energy landscape associated with the coordinates. Fep1d is a script for the analysis of such one-dimensional coordinates. The script allows one to construct conventional and cut-based free energy profiles, to assess the optimality of a reaction coordinate, to inspect whether the dynamics projected on the coordinate is diffusive, to transform (rescale) the reaction coordinate to more convenient ones, and to compute such quantities as the mean first passage time, the transition path times, the coordinate dependent diffusion coefficient, and so forth. Here, we describe the implemented functionality together with the underlying theoretical framework.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | (c) 2015, Wiley Periodicals, Inc. This is the peer reviewed version of the following article: Banushkina, PV and Krivov, SV (2015) Fep1d: A Script for the Analysis of Reaction Coordinates. Journal of Computational Chemistry, 36 (12). pp. 878-882, which has been published in final form at http://dx.doi.org/10.1002/jcc.23868. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving. |
Keywords: | reaction coordinate; free energy profile; diffusion; cut free energy profile; dimensionality reduction |
Dates: |
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Institution: | The University of Leeds |
Academic Units: | The University of Leeds > Faculty of Biological Sciences (Leeds) |
Depositing User: | Symplectic Publications |
Date Deposited: | 18 Apr 2016 11:00 |
Last Modified: | 03 Feb 2018 21:42 |
Published Version: | http://dx.doi.org/10.1002/jcc.23868 |
Status: | Published |
Publisher: | Wiley |
Identification Number: | 10.1002/jcc.23868 |
Related URLs: | |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:92529 |