ArticleJournal of chemical theory and computation2019
Fast Solver for Large Scale Multistate Bennett Acceptance Ratio Equations.
Article in Journal of chemical theory and computation, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
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- Sampling the Grand Canonical Ensemble with Multisite λ Dynamics.The journal of physical chemistry letters · 2026Article
- Free energy calculations in molecular modeling: from classical methods to machine learning.Journal of molecular modeling · 2026Review
- Knowledge Distillation of a Protein Language Model Yields a Foundational Implicit Solvent Model.ArXiv · 2026Article
- Simultaneous Construction of Free Energy Surfaces via Multisite λ Dynamics and Umbrella Sampling.Journal of chemical theory and computation · 2025Article
- Free energy spectroscopy reveals the mechanistic landscape of chromatin compaction.bioRxiv : the preprint server for biology · 2025Article
- Transient Poly(ADP-Ribose) Triggers FUS Condensation Hysteresis via a Prion-Like Mechanism.bioRxiv : the preprint server for biology · 2025Article
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- Scaling Graph Neural Networks to Large Proteins.Journal of chemical theory and computation · 2025Article
- Superimposing Ligands with a Ligand Overlay as an Alternate Topology Model for λ-Dynamics-Based Calculations.The journal of physical chemistry. B · 2024Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Exploring the Limits of the Generalized CHARMM and AMBER Force Fields through Predictions of Hydration Free Energy of Small Molecules.Journal of chemical information and modeling · 2024Article
- Bayesian Multistate Bennett Acceptance Ratio Methods.Journal of chemical theory and computation · 2024Article
- Enhanced Sampling of Buried Charges in Free Energy Calculations Using Replica Exchange with Charge Tempering.Journal of chemical theory and computation · 2024Article
- Biomolecular dynamics in the 21st century.Biochimica et biophysica acta. General subjects · 2024Review
- Computing equilibrium free energies through a nonequilibrium quench.The Journal of chemical physics · 2024Article
- Transferable Implicit Solvation via Contrastive Learning of Graph Neural Networks.ACS central science · 2023Article
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Authors and funding
3 authors.
Funding
Abstract
The multistate Bennett acceptance ratio method (MBAR) and unbinned weighted histogram analysis method (UWHAM) are widely employed approaches to calculate relative free energies of multiple thermodynamic states that gain statistical precision by employing free energy contributions from configurations sampled at each of the simulated λ states. With the increasing availability of high throughput computing resources, a large number of configurations can be sampled from hundreds or even thousands of states. Combining sampled configurations from all states to calculate relative free energies requires the iterative solution of large scale MBAR/UWHAM equations. In the current work, we describe the development of a fast solver to iteratively solve these large scale MBAR/UWHAM equations utilizing our previous findings that the MBAR/UWHAM equations can be derived as a Rao-Blackwell estimator. The solver is implemented and distributed as a Python module called FastMBAR. Our benchmark results show that FastMBAR is more than 2 times faster than the widely used solver pymbar, when it runs on a central processing unit (CPU) and more than 100 times faster than pymbar when it runs on a graphical processing unit (GPU). The significant speedup achieved by FastMBAR running on a GPU is useful not only for solving large scale MBAR/UWHAM equations but also for estimating uncertainty of calculated free energies using bootstrapping where the MBAR/UWHAM equations need to be solved multiple times.
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