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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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Publication details

The article was received on 09 May 2016, accepted on 14 Jun 2016 and first published on 14 Jun 2016


Article type: Paper
DOI: 10.1039/C6FD00124F
Citation: Faraday Discuss., 2016,195, 345-364
  • Open access: Creative Commons BY license
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    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

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