ArticleThe journal of physical chemistry. B2015
The adaptive biasing force method: everything you always wanted to know but were afraid to ask.
Article in The journal of physical chemistry. B, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 142 papers.
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Who cites it
142 citing papers in PubMed.
- DeepPath: overcoming data scarcity for protein transition pathway prediction using physics-based deep learning.Chemical science · 2026Article
- Functional Calmodulin States Are Selected from an Electrostatically Tuned Free Energy Landscape.Journal of chemical information and modeling · 2026Article
- Free-Energy Landscapes of HBV Hexamer Closure Reveal Key Structural Features of the Transition.Journal of chemical theory and computation · 2026Article
- De novo design of peptides localizing at the interface of biomolecular condensates.Nature communications · 2026Article
- Dual-LAO for calculating fast and robust relative binding free energies of simple and complex transformations.Communications chemistry · 2026Article
- ASH: A Multi-Scale, Multi-Theory Modeling Program.Journal of computational chemistry · 2026Article
- Structural and Kinetic Basis for the Rational Design of Next-Generation β-Lactamase Inhibitors.Journal of medicinal chemistry · 2026Article
- Article
- Reinforced molecular dynamics: Physics-infused generative machine learning model simulates protein motion.PNAS nexus · 2026Article
- Enhanced Sampling and Free Energy Calculations in Protein Simulations.Advances in experimental medicine and biology · 2026Review
- Quantum Chemistry Calculations of Circularly Polarized Luminescence (CPL): From Spectral Modeling to Molecular Design.Chemical reviews · 2025Review
- Entangled Schrödinger Bridge Matching.ArXiv · 2025Article
- Advancing active compound discovery for novel drug targets: insights from AI-driven approaches.Acta pharmacologica Sinica · 2025Review
- Calculating Free-Energy Differences Using an Average Force: A Tutorial for Adaptive Biasing Force Simulations.The journal of physical chemistry. B · 2025Article
- Influence of Membrane Composition on the Passive Membrane Penetration of Industrially Relevant NSO-Heterocycles.International journal of molecular sciences · 2025Article
- The String Method with Swarms of Trajectories: A Tutorial for Free-Energy Calculations Along a Zero-Drift Pathway.The journal of physical chemistry. B · 2025Article
- Combining Fast Exploration with Accurate Reweighting in the OPES-eABF Hybrid Sampling Method.Journal of chemical theory and computation · 2025Article
- The Q-AMOEBA (CF) Polarizable Potential.The journal of physical chemistry letters · 2025Article
- Dissecting Large-Scale Structural Transitions in Membrane Transporters Using Advanced Simulation Technologies.The journal of physical chemistry. B · 2025Review
- Improved Free-Energy Estimates for the Permeation of Bulky Antibiotic Molecules through Porin Channels Using Temperature-Accelerated Sliced Sampling.Journal of chemical theory and computation · 2025Article
82 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
Abstract
In the host of numerical schemes devised to calculate free energy differences by way of geometric transformations, the adaptive biasing force algorithm has emerged as a promising route to map complex free-energy landscapes. It relies upon the simple concept that as a simulation progresses, a continuously updated biasing force is added to the equations of motion, such that in the long-time limit it yields a Hamiltonian devoid of an average force acting along the transition coordinate of interest. This means that sampling proceeds uniformly on a flat free-energy surface, thus providing reliable free-energy estimates. Much of the appeal of the algorithm to the practitioner is in its physically intuitive underlying ideas and the absence of any requirements for prior knowledge about free-energy landscapes. Since its inception in 2001, the adaptive biasing force scheme has been the subject of considerable attention, from in-depth mathematical analysis of convergence properties to novel developments and extensions. The method has also been successfully applied to many challenging problems in chemistry and biology. In this contribution, the method is presented in a comprehensive, self-contained fashion, discussing with a critical eye its properties, applicability, and inherent limitations, as well as introducing novel extensions. Through free-energy calculations of prototypical molecular systems, many methodological aspects are examined, from stratification strategies to overcoming the so-called hidden barriers in orthogonal space, relevant not only to the adaptive biasing force algorithm but also to other importance-sampling schemes. On the basis of the discussions in this paper, a number of good practices for improving the efficiency and reliability of the computed free-energy differences are proposed.
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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.