ArticleThe Journal of chemical physics2015
Extracting the diffusion tensor from molecular dynamics simulation with Milestoning.
Article in The Journal of chemical physics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- ScMiles2: A Script to Conduct and Analyze Milestoning Trajectories for Long Time Dynamics.Journal of chemical theory and computation · 2022Article
- Ion Permeation through a Phospholipid Membrane: Transition State, Path Splitting, and Calculation of Permeability.Journal of chemical theory and computation · 2019Article
- Accurate Protein-Folding Transition-Path Statistics from a Simple Free-Energy Landscape.The journal of physical chemistry. B · 2018Article
- Single-Molecule Test for Markovianity of the Dynamics along a Reaction Coordinate.The journal of physical chemistry letters · 2018Article
- Communication: Coordinate-dependent diffusivity from single molecule trajectories.The Journal of chemical physics · 2017Article
- Pyrophosphate Release in the Protein HIV Reverse Transcriptase.The journal of physical chemistry. B · 2017Article
- Bridging scales through multiscale modeling: a case study on protein kinase A.Frontiers in physiology · 2015Review
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Authors and funding
2 authors.
Funding
Abstract
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.
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