TY - CHAP

T1 - Development of a massively parallel QM/MM approach combined with a theory of solutions

AU - Takahashi, Hideaki

AU - Matubayasi, Nobuyuki

PY - 2015/1/1

Y1 - 2015/1/1

N2 - In this contributed article we review our method, referred to as QM/MM-ER, which combines the hybrid QM/MM simulation with the theory of energy representation. Our recent developments and applications related to the method are also introduced. First, we describe the parallel implementation of the Kohn-Sham DFT for the QM region that utilizes the real-space grids to represent the one-electron wave functions. Then, the efficiency of our code on a modern parallel machine is demonstrated for a large water cluster with an ice structure. Secondly, the theory of energy representation (ER) is formulated within the framework of the density functional theory of solutions and its application to the free energy analyses of the protein hydration is provided. Thirdly, we discuss the coupling of the QM/MM approach with the method of energy representation, where the formulation for free energy δμ due to the electron density fluctuation of a QM solute plays a key role. As a recent progress in QM/MM-ER we developed a rigorous free energy functional to compute free energy contribution δμ. The outline of the method as well as its extension to the QM/MM simulation coupled with a second-order perturbation approach are described.

AB - In this contributed article we review our method, referred to as QM/MM-ER, which combines the hybrid QM/MM simulation with the theory of energy representation. Our recent developments and applications related to the method are also introduced. First, we describe the parallel implementation of the Kohn-Sham DFT for the QM region that utilizes the real-space grids to represent the one-electron wave functions. Then, the efficiency of our code on a modern parallel machine is demonstrated for a large water cluster with an ice structure. Secondly, the theory of energy representation (ER) is formulated within the framework of the density functional theory of solutions and its application to the free energy analyses of the protein hydration is provided. Thirdly, we discuss the coupling of the QM/MM approach with the method of energy representation, where the formulation for free energy δμ due to the electron density fluctuation of a QM solute plays a key role. As a recent progress in QM/MM-ER we developed a rigorous free energy functional to compute free energy contribution δμ. The outline of the method as well as its extension to the QM/MM simulation coupled with a second-order perturbation approach are described.

KW - Energy Distribution Function

KW - Energy Representation

KW - Hydration Free Energy

KW - Kinetic Energy Operator

KW - Solvation Free Energy

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UR - http://www.scopus.com/inward/citedby.url?scp=85073165666&partnerID=8YFLogxK

U2 - 10.1007/978-3-319-21626-3_6

DO - 10.1007/978-3-319-21626-3_6

M3 - Chapter

AN - SCOPUS:85073165666

T3 - Challenges and Advances in Computational Chemistry and Physics

SP - 153

EP - 196

BT - Challenges and Advances in Computational Chemistry and Physics

PB - Springer

ER -