title: Rapid QM/MM approach for biomolecular systems under periodic boundary conditions: Combination of the density-functional tight-binding theory and particle mesh Ewald method.
abstract: A quantum mechanical/molecular mechanical (QM/MM) approach based on the density-functional tight-binding (DFTB) theory is a useful tool for analyzing chemical reaction systems in detail. In this study, an efficient QM/MM method is developed by the combination of the DFTB/MM and particle mesh Ewald (PME) methods. Because the Fock matrix, which is required in the DFTB calculation, is analytically obtained by the PME method, the Coulomb energy is accurately and rapidly computed. For assessing the performance of this method, DFTB/MM calculations and molecular dynamics simulation are conducted for a system consisting of two amyloid-β(1-16) peptides and a zinc ion in explicit water under periodic boundary conditions. As compared with that of the conventional Ewald summation method, the computational cost of the Coulomb energy by utilizing the present approach is drastically reduced, i.e., 166.5 times faster. Furthermore, the deviation of the electronic energy is less than 10-6 Eh. © 2016 Wiley Periodicals, Inc.
authors.affiliation: Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Aichi, 444-8585, Japan.
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Nishizawa
authors.affiliation: Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Aichi, 444-8585, Japan. hokumura@ims.ac.jp.|Department of Structural Molecular Science, The Graduate University for Advanced Studies, Okazaki, Aichi, 444-8585, Japan. hokumura@ims.ac.jp.
authors.forename: Hisashi
authors.initials: H
authors.lastname: Okumura
keywords: biomolecule; density-functional tight-binding theory; molecular dynamics; particle mesh Ewald method; periodic boundary condition; quantum mechanical/molecular mechanical treatment