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Volume 195, 2016
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S-shooting: a Bennett–Chandler-like method for the computation of rate constants from committor trajectories

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Abstract

Mechanisms of rare transitions between long-lived stable states are often analyzed in terms of commitment probabilities, determined from swarms of short molecular dynamics trajectories. Here, we present a computer simulation method to determine rate constants from such short trajectories combined with free energy calculations. The method, akin to the Bennett–Chandler approach for the calculation of reaction rate constants, requires the definition of a valid reaction coordinate and can be applied to both under- and overdamped dynamics. We verify the correctness of the algorithm using a one-dimensional random walker in a double-well potential and demonstrate its applicability to complex transitions in condensed systems by calculating cavitation rates for water at negative pressures.

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Article information


Submitted
09 May 2016
Accepted
14 Jun 2016
First published
14 Jun 2016

This article is Open Access

Faraday Discuss., 2016,195, 345-364
Article type
Paper
Author version available

S-shooting: a Bennett–Chandler-like method for the computation of rate constants from committor trajectories

G. Menzl, A. Singraber and C. Dellago, Faraday Discuss., 2016, 195, 345 DOI: 10.1039/C6FD00124F

This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. You can use material from this article in other publications without requesting further permissions from the RSC, provided that the correct acknowledgement is given.

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