Calculating Iso-Committor Surfaces as Optimal Reaction Coordinates with Milestoning
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Institute for Computational Engineering and Science, The University of Texas at Austin, Austin, TX 78712, USA
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Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
*
Author to whom correspondence should be addressed.
Academic Editors: Giovanni Ciccotti, Mauro Ferrario and Christof Schuette
Entropy 2017, 19(5), 219; https://doi.org/10.3390/e19050219
Received: 17 February 2017
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Revised: 24 April 2017
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Accepted: 8 May 2017
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Published: 11 May 2017
(This article belongs to the Special Issue Understanding Molecular Dynamics via Stochastic Processes)
Reaction coordinates are vital tools for qualitative and quantitative analysis of molecular processes. They provide a simple picture of reaction progress and essential input for calculations of free energies and rates. Iso-committor surfaces are considered the optimal reaction coordinate. We present an algorithm to compute efficiently a sequence of isocommittor surfaces. These surfaces are considered an optimal reaction coordinate. The algorithm analyzes Milestoning results to determine the committor function. It requires only the transition probabilities between the milestones, and not transition times. We discuss the following numerical examples: (i) a transition in the Mueller potential; (ii) a conformational change of a solvated peptide; and (iii) cholesterol aggregation in membranes.
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Keywords:
order parameter; molecular dynamics; milestones; reaction pathways
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MDPI and ACS Style
Elber, R.; Bello-Rivas, J.M.; Ma, P.; Cardenas, A.E.; Fathizadeh, A. Calculating Iso-Committor Surfaces as Optimal Reaction Coordinates with Milestoning. Entropy 2017, 19, 219. https://doi.org/10.3390/e19050219
AMA Style
Elber R, Bello-Rivas JM, Ma P, Cardenas AE, Fathizadeh A. Calculating Iso-Committor Surfaces as Optimal Reaction Coordinates with Milestoning. Entropy. 2017; 19(5):219. https://doi.org/10.3390/e19050219
Chicago/Turabian StyleElber, Ron, Juan M. Bello-Rivas, Piao Ma, Alfredo E. Cardenas, and Arman Fathizadeh. 2017. "Calculating Iso-Committor Surfaces as Optimal Reaction Coordinates with Milestoning" Entropy 19, no. 5: 219. https://doi.org/10.3390/e19050219
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