Calculating Iso-Committor Surfaces as Optimal Reaction Coordinates with Milestoning

Calculating Iso-Committor Surfaces as Optimal Reaction Coordinates with Milestoning

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...

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Bibliographic Details
Main Authors: Ron Elber, Juan M. Bello-Rivas, Piao Ma, Alfredo E. Cardenas, Arman Fathizadeh
Format: Article
Language:English
Published: MDPI AG 2017-05-01
Series:Entropy
Subjects:
order parameter
molecular dynamics
milestones
reaction pathways
Online Access:http://www.mdpi.com/1099-4300/19/5/219
Description
Summary: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.
ISSN:1099-4300

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