title: Comparison of Methods To Reweight from Classical Molecular Simulations to QM/MM Potentials.
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.
authors.affiliation: Department of Chemical Engineering, University of Virginia , Charlottesville, Virginia 22904, United States.
authors.forename: Eric C
authors.initials: EC
authors.lastname: Dybeck
authors.affiliation: Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health , 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States.
authors.forename: Gerhard
authors.initials: G
authors.lastname: König
authors.affiliation: Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health , 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States.
authors.forename: Bernard R
authors.initials: BR
authors.lastname: Brooks
authors.affiliation: Department of Chemical Engineering, University of Virginia , Charlottesville, Virginia 22904, United States.|Department of Chemical and Biological Engineering, University of Colorado Boulder , Boulder, Colorado 80309, United States.
authors.forename: Michael R
authors.initials: MR
authors.lastname: Shirts
mesh_terms: D019187:Cadmium Compounds / Q000737:chemistry*; D004583:Electrons; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D037742:Nanotubes, Carbon / Q000737:chemistry*; D045663:Quantum Dots / Q000737:chemistry*; D011789:Quantum Theory; D018036:Selenium Compounds / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D019187:Cadmium Compounds; D037742:Nanotubes, Carbon; D018036:Selenium Compounds; C058667:cadmium selenide