ArticleThe Journal of chemical physics2015
Exact 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 59 papers.
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Who cites it
59 citing papers in PubMed.
- Reducing weighted ensemble variance with optimal trajectory management.The Journal of chemical physics · 2026Article
- Advances and Challenges in Milestoning Simulations for Drug-Target Kinetics.Journal of chemical theory and computation · 2024Article
- Generating Protein Structures for Pathway Discovery Using Deep Learning.Journal of chemical theory and computation · 2024Article
- BAD-NEUS: Rapidly converging trajectory stratification.The Journal of chemical physics · 2024Article
- Understanding the impact of binding free energy and kinetics calculations in modern drug discovery.Expert opinion on drug discovery · 2024Review
- Exploring Biomolecular Conformational Dynamics with Polarizable Force Field AMOEBA and Enhanced Sampling Method Milestoning.Journal of chemical theory and computation · 2024Article
- Milestoning estimators of dissipation in systems observed at a coarse resolution.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Targeted Protein Degradation: Advances, Challenges, and Prospects for Computational Methods.Journal of chemical information and modeling · 2023Review
- Weighted ensemble: Recent mathematical developments.The Journal of chemical physics · 2023Article
- Binding Kinetics Toolkit for Analyzing Transient Molecular Conformations and Computing Free Energy Landscapes.The journal of physical chemistry. A · 2022Article
- Perspective: Path Sampling Methods Applied to Enzymatic Catalysis.Journal of chemical theory and computation · 2022Review
- ScMiles2: A Script to Conduct and Analyze Milestoning Trajectories for Long Time Dynamics.Journal of chemical theory and computation · 2022Article
- Computing transition path theory quantities with trajectory stratification.The Journal of chemical physics · 2022Article
- SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine.Journal of chemical information and modeling · 2022Article
- Gaussian-Accelerated Molecular Dynamics with the Weighted Ensemble Method: A Hybrid Method Improves Thermodynamic and Kinetic Sampling.Journal of chemical theory and computation · 2021Article
- Dissecting Multiple Pathways in the Relaxation Dynamics of Helix <==> Coil Transitions with Optimum Dimensionality Reduction.Biomolecules · 2021Review
- Impact of the Protonation State of Phosphatidylinositol 4,5-Bisphosphate (PIP2) on the Binding Kinetics and Thermodynamics to Transient Receptor Potential Vanilloid (TRPV5): A Milestoning Study.The journal of physical chemistry. B · 2021Article
- Computer Simulations of the Dissociation Mechanism of Gleevec from Abl Kinase with Milestoning.The journal of physical chemistry. B · 2021Article
- What Markov State Models Can and Cannot Do: Correlation versus Path-Based Observables in Protein-Folding Models.Journal of chemical theory and computation · 2021Article
- Value of Temporal Information When Analyzing Reaction Coordinates.Journal of chemical theory and computation · 2020Article
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Authors and funding
2 authors.
Funding
Abstract
A new theory and an exact computer algorithm for calculating kinetics and thermodynamic properties of a particle system are described. The algorithm avoids trapping in metastable states, which are typical challenges for Molecular Dynamics (MD) simulations on rough energy landscapes. It is based on the division of the full space into Voronoi cells. Prior knowledge or coarse sampling of space points provides the centers of the Voronoi cells. Short time trajectories are computed between the boundaries of the cells that we call milestones and are used to determine fluxes at the milestones. The flux function, an essential component of the new theory, provides a complete description of the statistical mechanics of the system at the resolution of the milestones. We illustrate the accuracy and efficiency of the exact Milestoning approach by comparing numerical results obtained on a model system using exact Milestoning with the results of long trajectories and with a solution of the corresponding Fokker-Planck equation. The theory uses an equation that resembles the approximate Milestoning method that was introduced in 2004 [A. K. Faradjian and R. Elber, J. Chem. Phys. 120(23), 10880-10889 (2004)]. However, the current formulation is exact and is still significantly more efficient than straightforward MD simulations on the system studied.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.