Adaptive-Partitioning Redistributed Charge and Dipole Schemes for QM/MM Dynamics Simulations: On-the-fly Relocation of Boundaries that Pass through Covalent Bonds.

Abstract

Recently, Heyden, Lin, and Truhlar (J. Phys. Chem. B2007, 111, 2231-2241) formularized the adaptive-partitioning schemes for quantum mechanical and molecular mechanical (QM/MM) molecular dynamics simulations. The adaptive-partitioning schemes permit on-the-fly reclassification of atoms/groups as part of the QM or MM subsystems during dynamics simulations. Test simulations of argon atoms in a periodic box with dual-level MM potentials in the microcanonical ensemble demonstrated that the adaptive-partitioning schemes conserved energy and momentum, which is critical to ensure correct sampling of configuration spaces of desired ensembles. In this work, we reported the extension of the adaptive-partitioning schemes to deal with groups that are molecular fragments. The newly developed adaptive-partitioning redistributed charge scheme and adaptive-partitioning redistributed charge and dipole schemes allow on-the-fly relocation of the QM/MM boundaries that cut through covalent bonds during dynamics simulations. Test QM/MM simulations with a variety of QM levels of theory in the microcanonical ensembles demonstrated that the new schemes conserve energy and momentum.