ArticleJournal of chemical theory and computation2010
Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables.
Article in Journal of chemical theory and computation, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 114 papers.
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Who cites it
114 citing papers in PubMed.
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- Role of viral protein ratio in the structure and separation of empty and full adeno-associated virus capsids: A molecular dynamics study.Molecular therapy. Advances · 2026Article
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- Iduronate Ring Puckering Effects on Preferred Glycosidic Linkage Conformations in Heparin/Heparan Sulfate and Dermatan Sulfate Disaccharides.Molecules (Basel, Switzerland) · 2026Article
- Monosaccharide-Derived Enantioselectivity in SWCNT Chemoresistive VOC Sensing.Chemistry (Weinheim an der Bergstrasse, Germany) · 2025Article
- Characterization of an Open-Channel Structure and Lateral Conduction Pathway in the Cation-Selective Pentameric Ligand-Gated Ion Channel, ELIC.bioRxiv : the preprint server for biology · 2025Article
- Calculating Free-Energy Differences Using an Average Force: A Tutorial for Adaptive Biasing Force Simulations.The journal of physical chemistry. B · 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
- A Gaussian kernel Monte Carlo resampling method to construct smooth free energy surface from discrete simulation data.The Journal of chemical physics · 2025Article
- Molecular Insights into the Adsorption of Deposit Control Additives from Hydrocarbon Fuels.Langmuir : the ACS journal of surfaces and colloids · 2025Article
- Expanded Functionality and Portability for the Colvars Library.The journal of physical chemistry. B · 2024Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Statistical Mechanical Theories of Membrane Permeability.The journal of physical chemistry. B · 2024Article
- Membrane Stabilization of Helical Previtamin D Conformers as Possible Enhancement of Vitamin D Photoproduction.The journal of physical chemistry. B · 2024Article
- An Atomic and Molecular Insight into How PFOA Reduces α-Helicity, Compromises Substrate Binding, and Creates Binding Pockets in a Model Globular Protein.Journal of the American Chemical Society · 2024Article
54 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
A new implementation of the adaptive biasing force (ABF) method is described. This implementation supports a wide range of collective variables and can be applied to the computation of multidimensional energy profiles. It is provided to the community as part of a code that implements several analogous methods, including metadynamics. ABF and metadynamics have not previously been tested side by side on identical systems. Here, numerical tests are carried out on processes including conformational changes in model peptides and translocation of a halide ion across a lipid membrane through a peptide nanotube. On the basis of these examples, we discuss similarities and differences between the ABF and metadynamics schemes. Both approaches provide enhanced sampling and free energy profiles in quantitative agreement with each other in different applications. The method of choice depends on the dimension of the reaction coordinate space, the height of the barriers, and the relaxation times of degrees of freedom in the orthogonal space, which are not explicitly described by the chosen collective variables.
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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.