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Extracting the diffusion tensor from molecular dynamics simulation with Milestoning
- Source :
- The Journal of Chemical Physics. 142:014105
- Publication Year :
- 2015
- Publisher :
- AIP Publishing, 2015.
-
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.
- Subjects :
- Physics
Alanine
Computation
Solvation
General Physics and Astronomy
Dipeptides
Molecular Dynamics Simulation
Kinetic energy
Diffusion
ARTICLES
Molecular dynamics
Classical mechanics
Master equation
Fokker–Planck equation
Statistical physics
Physical and Theoretical Chemistry
Potential of mean force
Algorithms
Diffusion MRI
Subjects
Details
- ISSN :
- 10897690 and 00219606
- Volume :
- 142
- Database :
- OpenAIRE
- Journal :
- The Journal of Chemical Physics
- Accession number :
- edsair.doi.dedup.....2fb70569ab51b5e93a45ce8ceb853366
- Full Text :
- https://doi.org/10.1063/1.4904882