ArticleJournal of chemical theory and computation2016
Comparison of Methods To Reweight from Classical Molecular Simulations to QM/MM Potentials.
Article in Journal of chemical theory and computation, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Machine Learning-Enhanced Calculation of Quantum-Classical Binding Free Energies.Journal of chemical theory and computation · 2025Article
- Effects of Conformational Sampling on Computing Redox Properties Using Linear Response Approach.The journal of physical chemistry. B · 2025Article
- Free energies at QM accuracy from force fields via multimap targeted estimation.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Accurate and Efficient Multilevel Free Energy Simulations with Neural Network-Assisted Enhanced Sampling.Journal of chemical theory and computation · 2023Article
- Perspective: Reference-Potential Methods for the Study of Thermodynamic Properties in Chemical Processes: Theory, Applications, and Pitfalls.The journal of physical chemistry letters · 2023Review
- AffordableThe journal of physical chemistry. A · 2021Article
- Accelerated Computation of Free Energy Profile atJournal of chemical theory and computation · 2021Article
- 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
- Best Practices for Alchemical Free Energy Calculations [Article v1.0].Living journal of computational molecular science · 2020Article
- Development of a Robust Indirect Approach for MM → QM Free Energy Calculations That Combines Force-Matched Reference Potential and Bennett's Acceptance Ratio Methods.Journal of chemical theory and computation · 2019Article
- Scalable Indirect Free Energy Method Applied to Divalent Cation-Metalloprotein Binding.Journal of chemical theory and computation · 2019Article
- Use of Interaction Energies in QM/MM Free Energy Simulations.Journal of chemical theory and computation · 2019Article
- A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes.Molecules (Basel, Switzerland) · 2018Article
- On the convergence of multi-scale free energy simulations.Molecular simulation · 2018Article
- Toward polarizable AMOEBA thermodynamics at fixed charge efficiency using a dual force field approach: application to organic crystals.Physical chemistry chemical physics : PCCP · 2016Article
- Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pKJournal of computer-aided molecular design · 2016Article
- Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challenge.Journal of computer-aided molecular design · 2016Article
- An efficient protocol for obtaining accurate hydration free energies using quantum chemistry and reweighting from molecular dynamics simulations.Bioorganic & medicinal chemistry · 2016Article
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4 authors.
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Abstract
We examine methods to reweight classical molecular mechanics solvation calculations to more expensive QM/MM energy functions. We first consider the solvation free energy difference between ethane and methanol in a QM/MM Hamiltonian from configurations generated in a cheaper MM potential. The solute molecules in the QM/MM Hamiltonian are treated with B3LYP/6-31G*, and the solvent water molecules are treated classically. The free energy difference in the QM/MM Hamiltonian is estimated using Boltzmann reweighting with both the non-Boltzmann Bennett method (NBB) and the multistate Bennett acceptance ratio (MBAR), and the variance of each method is directly compared for an identical data set. For this system, MBAR-derived methods are found to produce smaller overall uncertainties than NBB-based methods. Additionally, we show that to reduce the variance in the overall free energy difference estimate in this system for a fixed amount of QM/MM calculations, the energy re-evaluations in the Boltzmann reweighting step should be concentrated on the physical MM states with the highest overlap to the QM/MM states, rather than allocated equally over all sampled MM states. We also show that reallocating the QM/MM re-evaluations can be used to diagnose poor overlap between the sampled and target state. The solvation free energies for molecules in the SAMPL4 solvation data set are also calculated in the QM/MM Hamiltonian with NBB and MBAR, and the variances are marginally smaller for MBAR. Overall, NBB and MBAR produce similar variances for systems with poor sampling efficiency, and MBAR provides smaller variances than NBB in systems with high sampling efficiency. Both NBB and MBAR converge to identical solvation free energy estimates in the QM/MM Hamiltonian, and the RMSD to experimental values for molecules in the SAMPL4 solvation data set decreases by approximately 28% when switching from the MM Hamiltonian to the QM/MM Hamiltonian.
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