ArticleJournal of chemical theory and computation2013
w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations.
Article in Journal of chemical theory and computation, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Origins of Reactivity in SAM-Utilizing Ribozyme SAMURI-Catalyzed RNA Alkylation.Journal of the American Chemical Society · 2026Article
- AMBER Free Energy Tools: A New Framework for the Design of Optimized Alchemical Transformation Pathways.Journal of chemical theory and computation · 2023Article
- CHARMM-GUI Enhanced Sampler for various collective variables and enhanced sampling methods.Protein science : a publication of the Protein Society · 2022Article
- Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery.Journal of chemical information and modeling · 2020Article
- Improved Alchemical Free Energy Calculations with Optimized Smoothstep Softcore Potentials.Journal of chemical theory and computation · 2020Article
- Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network.Journal of chemical information and modeling · 2019Article
- GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features.Journal of chemical information and modeling · 2018Article
- Improving Prediction Accuracy of Binding Free Energies and Poses of HIV Integrase Complexes Using the Binding Energy Distribution Analysis Method with Flattening Potentials.Journal of chemical information and modeling · 2018Article
- Gaussian Accelerated Molecular Dynamics: Theory, Implementation, and Applications.Annual reports in computational chemistry · 2017Article
- Simulating Replica Exchange: Markov State Models, Proposal Schemes, and the Infinite Swapping Limit.The journal of physical chemistry. B · 2016Article
- Binding Energy Distribution Analysis Method: Hamiltonian Replica Exchange with Torsional Flattening for Binding Mode Prediction and Binding Free Energy Estimation.Journal of chemical theory and computation · 2016Article
- Locally weighted histogram analysis and stochastic solution for large-scale multi-state free energy estimation.The Journal of chemical physics · 2016Article
- The true nature of rotary movements in rotaxanes.Chemical science · 2016Article
- Asynchronous Replica Exchange Software for Grid and Heterogeneous Computing.Computer physics communications · 2015Article
- Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach.Chemphyschem : a European journal of chemical physics and physical chemistry · 2015Article
- Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis.Journal of computational chemistry · 2015Article
- How to deal with multiple binding poses in alchemical relative protein-ligand binding free energy calculations.Journal of chemical theory and computation · 2015Article
- Enhanced ligand sampling for relative protein-ligand binding free energy calculations.The journal of physical chemistry. B · 2015Article
- Characterization of the three-dimensional free energy manifold for the uracil ribonucleoside from asynchronous replica exchange simulations.Journal of chemical theory and computation · 2015Article
- Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation.Journal of chemical theory and computation · 2014Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Free energy governs the equilibrium extent of many biological processes. High barriers separating free energy minima often limit the sampling in molecular dynamics (MD) simulations, leading to inaccurate free energies. Here, we demonstrate enhanced sampling and improved free energy calculations, relative to conventional MD, using windowed accelerated MD within a Hamiltonian replica exchange framework (w-REXAMD). We show that for a case in which multiple conformations are separated by large free energy barriers, w-REXAMD is a useful enhanced sampling technique, without any necessary reweighting.
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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.