ArticleThe Journal of chemical physics2017
Rock climbing: A local-global algorithm to compute minimum energy and minimum free energy pathways.
Article in The Journal of chemical physics, 2017. 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.
- Thermodynamic and Kinetic Analysis of Molecular Conformational Dynamics in a Riemannian Framework.The journal of physical chemistry. A · 2026Article
- Comprehensive Approach to Simulating Large Scale Conformational Changes in Biological Systems Utilizing a Path Collective Variable and New Barrier Restraint.The journal of physical chemistry. B · 2023Article
- TYROSINE KINASES: COMPLEX MOLECULAR SYSTEMS CHALLENGING COMPUTATIONAL METHODOLOGIES.The European physical journal. B · 2021Article
- Molecular Dynamics-Based Thermodynamic and Kinetic Characterization of Membrane Protein Conformational Transitions.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Value of Temporal Information When Analyzing Reaction Coordinates.Journal of chemical theory and computation · 2020Article
- The transition between active and inactive conformations of Abl kinase studied by rock climbing and Milestoning.Biochimica et biophysica acta. General subjects · 2020Article
- Defect-Assisted Permeation Through a Phospholipid Membrane: Experimental and Computational Study of the Peptide WKW.The journal of physical chemistry. B · 2019Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
The calculation of minimum energy or minimum free energy paths is an important step in the quantitative and qualitative studies of chemical and physical processes. The computations of these coordinates present a significant challenge and have attracted considerable theoretical and computational interest. Here we present a new local-global approach to study reaction coordinates, based on a gradual optimization of an action. Like other global algorithms, it provides a path between known reactants and products, but it uses a local algorithm to extend the current path in small steps. The local-global approach does not require an initial guess to the path, a major challenge for global pathway finders. Finally, it provides an exact answer (the steepest descent path) at the end of the calculations. Numerical examples are provided for the Mueller potential and for a conformational transition in a solvated ring system.
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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.