ArticleJournal of computer-aided molecular design2014
Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge.
Article in Journal of computer-aided molecular design, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Insights and Challenges in Correcting Force Field Based Solvation Free Energies Using a Neural Network Potential.The journal of physical chemistry. B · 2024Article
- Fragmentation Method for Computing Quantum Mechanics and Molecular Mechanics Gradients for Force Matching: Validation with Hydration Free Energy Predictions Using Adaptive Force Matching.The journal of physical chemistry. A · 2022Article
- 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
- On the faithfulness of molecular mechanics representations of proteins towards quantum-mechanical energy surfaces.Interface focus · 2020Article
- Predicting partition coefficients of drug-like molecules in the SAMPL6 challenge with Drude polarizable force fields.Journal of computer-aided molecular design · 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
- Use of Interaction Energies in QM/MM Free Energy Simulations.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
- The Good, the Bad, and the Ugly: "HiPen", a New Dataset for Validating (S)QM/MM Free Energy Simulations.Molecules (Basel, Switzerland) · 2019Article
- Accelerating QM/MM Free Energy Computations via Intramolecular Force Matching.Journal of chemical theory and computation · 2018Article
- Force matching as a stepping stone to QM/MM CB[8] host/guest binding free energies: a SAMPL6 cautionary tale.Journal of computer-aided molecular design · 2018Article
- Multiscale Methods in Drug Design Bridge Chemical and Biological Complexity in the Search for Cures.Nature reviews. Chemistry · 2018Article
- Bayesian Model Averaging for Ensemble-Based Estimates of Solvation-Free Energies.The journal of physical chemistry. B · 2017Article
- Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level.Journal of computational chemistry · 2016Article
- Comparison of Methods To Reweight from Classical Molecular Simulations to QM/MM Potentials.Journal of chemical theory and computation · 2016Article
- Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical Method.Journal of chemical theory and computation · 2016Article
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4 authors.
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Abstract
We present our predictions for the SAMPL4 hydration free energy challenge. Extensive all-atom Monte Carlo simulations were employed to sample the compounds in explicit solvent. While the focus of our study was to demonstrate well-converged and reproducible free energies, we attempted to address the deficiencies in the general Amber force field force field with a simple QM/MM correction. We show that by using multiple independent simulations, including different starting configurations, and enhanced sampling with parallel tempering, we can obtain well converged hydration free energies. Additional analysis using dihedral angle distributions, torsion-root mean square deviation plots and thermodynamic cycles support this assertion. We obtain a mean absolute deviation of 1.7 kcal mol(-1) and a Kendall's τ of 0.65 compared with experiment.
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