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Rapid QM/MM approach for biomolecular systems under periodic boundary conditions: Combination of the density-functional tight-binding theory and particle mesh Ewald method.

H. Nishizawa, and H. Okumura. J. Comput. Chem., 37 (31): 2701-2711 (2016)

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Hisashi Saeki

Hisashi Ochi

Hisashi Saito

Hisashi Sugiura

Hisashi Yano

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Hamiltonian replica-permutation method and its applications to an alanine dipeptide and amyloid-β(29-42) peptides.S. Itoh, and H. Okumura. J. Comput. Chem., 34 (29): 2493-2497 (2013)Replica sub-permutation method for molecular dynamics and monte carlo simulations.M. Yamauchi, and H. Okumura. J. Comput. Chem., 40 (31): 2694-2711 (2019)Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweighting.H. Okumura, E. Gallicchio, and R. Levy. J. Comput. Chem., 31 (7): 1357-1367 (2010)Transformation between α-helix and β-sheet structures of one and two polyglutamine peptides in explicit water molecules by replica-exchange molecular dynamics simulations.H. Chiang, C. Chen, H. Okumura, and C. Hu. J. Comput. Chem., 35 (19): 1430-1437 (2014)Implementations of replica-permutation and replica sub-permutation methods into LAMMPS.M. Yamauchi, G. Penna, S. Itoh, and H. Okumura. Comput. Phys. Commun., (2022)Simulated tempering based on global balance or detailed balance conditions: Suwa-Todo, heat bath, and Metropolis algorithms.Y. Mori, and H. Okumura. J. Comput. Chem., 36 (31): 2344-2349 (2015)Rapid QM/MM approach for biomolecular systems under periodic boundary conditions: Combination of the density-functional tight-binding theory and particle mesh Ewald method.H. Nishizawa, and H. Okumura. J. Comput. Chem., 37 (31): 2701-2711 (2016)Coulomb replica-exchange method: Handling electrostatic attractive and repulsive forces for biomolecules.S. Itoh, and H. Okumura. J. Comput. Chem., 34 (8): 622-639 (2013)Ingenuity in performing replica permutation: How to order the state labels for improving sampling efficiency.D. Fukuhara, M. Yamauchi, S. Itoh, and H. Okumura. J. Comput. Chem., 44 (4): 534-545 (February 2023)New expression of the bulk viscosityH. Okumura, and F. Yonezawa. Physica A: Statistical Mechanics and its Applications, 321 (1-2): 207--219 (Apr 1, 2003)