ArticleMolecular simulation
QM/MM free energy simulations: recent progress and challenges.
Article in Molecular simulation. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed.
- Solvent Stabilization of Protic Oxonium/Ammonium Intermediates in Cation Radical Cyclization Reactions Investigated via Computational Approaches.The Journal of organic chemistry · 2026Article
- Quantum-Centric Alchemical Free Energy Calculations.Journal of chemical theory and computation · 2026Article
- Systematically Improvable and Locality Accelerated Enzymatic Reactivity Modeling: Toward Chemical Accuracy at Affordable Cost.Journal of chemical theory and computation · 2026Article
- Conformationally gated multisite proton-coupled electron transfer in the ribonucleotide reductaseProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Quantum Chemistry in Drug Design: Applications, Challenges, and the Need for Speed.Methods in molecular biology (Clifton, N.J.) · 2026Review
- Data-driven enhanced sampling of mechanistic pathways.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Computational Electrosynthesis: A Perspective on Mechanistic Questions, Methodological Approaches, and Elucidating the Role of the Electrical Double Layer.The journal of physical chemistry. C, Nanomaterials and interfaces · 2025Review
- Special Issue: "Advanced Research on Molecular Modeling of Protein Structure and Functions".International journal of molecular sciences · 2025Article
- In Silico ADME Methods Used in the Evaluation of Natural Products.Pharmaceutics · 2025Review
- Machine learning in molecular biophysics: Protein allostery, multi-level free energy simulations, and lipid phase transitions.Biophysics reviews · 2025Review
- Fine-tuning molecular mechanics force fields to experimental free energy measurements.bioRxiv : the preprint server for biology · 2025Article
- Catalytic Role of Methanol in Anodic Coupling Reactions Involving Alcohol Trapping of Cation Radicals.The Journal of organic chemistry · 2024Article
- Protocols for Metallo- and Serine-β-Lactamase Free Energy Predictions: Insights from Cross-Class Inhibitors.The journal of physical chemistry. B · 2024Article
- Nuclear Quantum Effects in Quantum Mechanical/Molecular Mechanical Free Energy Simulations of Ribonucleotide Reductase.Journal of the American Chemical Society · 2024Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Insights and Challenges in Correcting Force Field Based Solvation Free Energies Using a Neural Network Potential.The journal of physical chemistry. B · 2024Article
- Article
- Accurate and Efficient Multilevel Free Energy Simulations with Neural Network-Assisted Enhanced Sampling.Journal of chemical theory and computation · 2023Article
- Emerging Trends of Computational Chemistry and Molecular Modeling in Froth Flotation: A Review.ACS engineering Au · 2023Review
- MoBioTools: A toolkit to setup quantum mechanics/molecular mechanics calculations.Journal of computational chemistry · 2023Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Due to the higher computational cost relative to pure molecular mechanical (MM) simulations, hybrid quantum mechanical/molecular mechanical (QM/MM) free energy simulations particularly require a careful consideration of balancing computational cost and accuracy. Here we review several recent developments in free energy methods most relevant to QM/MM simulations and discuss several topics motivated by these developments using simple but informative examples that involve processes in water. For chemical reactions, we highlight the value of invoking enhanced sampling technique (e.g., replica-exchange) in umbrella sampling calculations and the value of including collective environmental variables (e.g., hydration level) in metadynamics simulations; we also illustrate the sensitivity of string calculations, especially free energy along the path, to various parameters in the computation. Alchemical free energy simulations with a specific thermodynamic cycle are used to probe the effect of including the first solvation shell into the QM region when computing solvation free energies. For cases where high-level QM/MM potential functions are needed, we analyze two different approaches: the QM/MM-MFEP method of Yang and co-workers and perturbative correction to low-level QM/MM free energy results. For the examples analyzed here, both approaches seem productive although care needs to be exercised when analyzing the perturbative corrections.
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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.