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Title: Extracting the diffusion tensor from molecular dynamics simulation with Milestoning

We propose an algorithm to extract the diffusion tensor from Molecular Dynamics simulations with Milestoning. A Kramers-Moyal expansion of a discrete master equation, which is the Markovian limit of the Milestoning theory, determines the diffusion tensor. To test the algorithm, we analyze overdamped Langevin trajectories and recover a multidimensional Fokker-Planck equation. The recovery process determines the flux through a mesh and estimates local kinetic parameters. Rate coefficients are converted to the derivatives of the potential of mean force and to coordinate dependent diffusion tensor. We illustrate the computation on simple models and on an atomically detailed system—the diffusion along the backbone torsions of a solvated alanine dipeptide.
Authors:
 [1] ;  [1] ;  [2]
  1. Department of Chemistry, University of Texas at Austin, Austin, Texas 78712 (United States)
  2. (United States)
Publication Date:
OSTI Identifier:
22415451
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Chemical Physics; Journal Volume: 142; Journal Issue: 1; Other Information: (c) 2015 AIP Publishing LLC; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; ALANINES; ALGORITHMS; COMPUTERIZED SIMULATION; COORDINATES; DIFFUSION; EXPANSION; FOKKER-PLANCK EQUATION; MARKOV PROCESS; MOLECULAR DYNAMICS METHOD; POTENTIALS; TENSORS; TORSION; TRAJECTORIES