title: Adaptive-partitioning QM/MM for molecular dynamics simulations: 4. Proton hopping in bulk water.
abstract: By reclassifying atoms as QM or MM on-the-fly, adaptive QM/MM dynamics simulations can utilize small QM subsystems whose locations and contents are continuously and automatically updated. Although adaptive QM/MM has been applied in studies of a variety of ions, dynamics simulations of a hydrated proton in bulk water remain a challenge. The difficulty arises from the need to transfer structural features (the covalent and hydrogen bonding networks) via the Grotthuss mechanism instead of the given proton. One must therefore identify an appropriate reference point from which the QM subsystem can be positioned that continuously follows the structural variations as the proton hops. To solve this problem, we propose a proton indicator that serves as the needed reference point. The location of the proton indicator varies smoothly from the hydronium oxygen in the resting (Eigen) state to the shared proton in the transition (Zundel) state. The algorithm is implemented in the framework of a modified permuted adaptive-partitioning QM/MM. As a proof of concept, we simulate an excess proton solvated in bulk water, where the QM subsystem is defined as a sphere of 4.0 Å radius centered at the proton indicator. We find that the use of the proton indicator prevents abrupt changes in the location and contents of the QM subsystem. The new method yields reasonably good agreement in the proton solvation structure and in the proton transfer dynamics with previously reported conventional QM/MM dynamics simulations that employed a much larger QM subsystem (a sphere of 12 Å radius). Also, the results do not change significantly with respect to variations in the time step size (0.1 or 0.5 fs), truncation of the many-body expansion of the potential (from fifth to second order), and absence/presence of thermostat. The proton indicator combined with the modified permuted adaptive-partitioning scheme thus appears to be a useful tool for studying proton transfer in solution.
authors.affiliation: Chemistry Department, University of Colorado Denver , Denver, Colorado 80217-3364, United States.
authors.forename: Soroosh
authors.initials: S
authors.lastname: Pezeshki
authors.affiliation: Chemistry Department, University of Colorado Denver , Denver, Colorado 80217-3364, United States.
authors.forename: Hai
authors.initials: H
authors.lastname: Lin