ArticleJournal of chemical theory and computation2018
Accelerating QM/MM Free Energy Computations via Intramolecular Force Matching.
Article in Journal of chemical theory and computation, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Quantum-Centric Alchemical Free Energy Calculations.Journal of chemical theory and computation · 2026Article
- Fully Atomistic Modeling in Computational Spectroscopy: Tryptophan in Aqueous Solution as a Test Case.The journal of physical chemistry. A · 2025Article
- Machine learning in molecular biophysics: Protein allostery, multi-level free energy simulations, and lipid phase transitions.Biophysics reviews · 2025Review
- Accurate and Efficient Multilevel Free Energy Simulations with Neural Network-Assisted Enhanced Sampling.Journal of chemical theory and computation · 2023Article
- Bridging semiempirical and ab initio QM/MM potentials by Gaussian process regression and its sparse variants for free energy simulation.The Journal of chemical physics · 2023Article
- Exploring Routes to Enhance the Calculation of Free Energy Differences via Non-Equilibrium Work SQM/MM Switching Simulations Using Hybrid Charge Intermediates between MM and SQM Levels of Theory or Non-Linear Switching Schemes.Molecules (Basel, Switzerland) · 2023Article
- Optimizing the Calculation of Free Energy Differences in Nonequilibrium Work SQM/MM Switching Simulations.The journal of physical chemistry. B · 2022Article
- Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches.Journal of computer-aided molecular design · 2022Article
- AffordableThe journal of physical chemistry. A · 2021Article
- Performing Molecular Dynamics Simulations and Computing Hydration Free Energies on the B3LYP-D3(BJ) Potential Energy Surface with Adaptive Force Matching: A Benchmark Study with Seven Alcohols and One Amine.ACS physical chemistry Au · 2021Article
- A comparison of three DFT exchange-correlation functionals and two basis sets for the prediction of the conformation distribution of hydrated polyglycine.The Journal of chemical physics · 2021Article
- Reaction Path-Force Matching in Collective Variables: Determining Ab Initio QM/MM Free Energy Profiles by Fitting Mean Force.Journal of chemical theory and computation · 2021Article
- A replica exchange umbrella sampling (REUS) approach to predict host-guest binding free energies in SAMPL8 challenge.Journal of computer-aided molecular design · 2021Article
- Accelerated Computation of Free Energy Profile atJournal of chemical theory and computation · 2021Article
- Biomolecular QM/MM Simulations: What Are Some of the "Burning Issues"?The journal of physical chemistry. B · 2021Article
- Accurate MP2-based force fields predict hydration free energies for simple alkanes and alcohols in good agreement with experiments.The Journal of chemical physics · 2020Article
- On the faithfulness of molecular mechanics representations of proteins towards quantum-mechanical energy surfaces.Interface focus · 2020Article
- What Does the Brønsted Slope Measure in the Phosphoryl Transfer Transition State?ACS catalysis · 2020Article
- Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery.Journal of chemical information and modeling · 2020Article
- Accelerated Computation of Free Energy Profile atJournal of chemical theory and computation · 2020Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
The calculation of free energy differences between levels of theory has numerous potential pitfalls. Chief among them is the lack of overlap, i.e., ensembles generated at one level of theory (e.g., "low") not being good approximations of ensembles at the other (e.g., "high"). Numerous strategies have been devised to mitigate this issue. However, the most straightforward approach is to ensure that the "low" level ensemble more closely resembles that of the "high". Ideally, this is done without increasing computational cost. Herein, we demonstrate that by reparametrizing classical intramolecular potentials to reproduce high level forces (i.e., force matching) configurational overlap between a "low" (i.e., classical) and "high" (i.e., quantum) level can be significantly improved. This procedure is validated on two test cases and results in vastly improved convergence of free energy simulations.
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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.