Zobrazeno 1 - 10
of 56
pro vyhledávání: '"Noriyuki Yoshii"'
Autor:
Yoshimichi Andoh, Shin-ichi Ichikawa, Tatsuya Sakashita, Kazushi Fujimoto, Noriyuki Yoshii, Tetsuro Nagai, Zhiye Tang, Susumu Okazaki
Publikováno v:
The Journal of Chemical Physics. 158
A new version of the highly parallelized general-purpose molecular dynamics (MD) simulation program MODYLAS with high performance on the Fugaku computer was developed. A benchmark test using Fugaku indicated highly efficient communication, single ins
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cca76ee068fe098fbca389d2c88e4737
https://doi.org/10.1063/5.0144361
https://doi.org/10.1063/5.0144361
Publikováno v:
Journal of Computational Chemistry. 41:940-948
We derived a new expression for the electrostatic interaction of three-dimensional charge-neutral systems with two-dimensional periodic boundary conditions (slab geometry) using a fast multipole method (FMM). Contributions from all the image cells ar
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b73f14cfc0f2839124339d43f5303703
https://doi.org/10.1002/jcc.26141
https://doi.org/10.1002/jcc.26141
Publikováno v:
Journal of computational chemistryREFERENCES. 42(15)
In the era of exascale supercomputers, large-scale, and long-time molecular dynamics (MD) calculations are expected to make breakthroughs in various fields of science and technology. Here, we propose a new algorithm to improve the parallelization per
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5153189438eea2a11dfcbef0484b2ecd
https://pubmed.ncbi.nlm.nih.gov/33780021
https://pubmed.ncbi.nlm.nih.gov/33780021
Publikováno v:
The Journal of chemical physics. 152(24)
In the molecular dynamics calculations for the free energy of ions and ionic molecules, we often encounter wet charged molecular systems where electrical neutrality condition is broken. This causes a problem in the evaluation of electrostatic interac
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5b324890d575ef5d7da3a17fba4c6cbf
https://pubmed.ncbi.nlm.nih.gov/32610973
https://pubmed.ncbi.nlm.nih.gov/32610973
Autor:
Susumu Okazaki, Masao Ogino, Tatsuya Sakashita, Satoshi Ohshima, Noriyuki Yoshii, Yoshimichi Andoh, Soichiro Suzuki, Takahiro Katagiri
Publikováno v:
The Journal of Supercomputing. 74:2449-2469
In molecular dynamics (MD) simulations, calculations of potentials and their derivatives by coordinate, i.e., forces, in a pairwise additive manner such as the Lennard–Jones interactions and a short-range part of the Coulombic interactions form the
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::b44d1e4e3a53b599086648732d34d86a
https://doi.org/10.1007/s11227-018-2272-2
https://doi.org/10.1007/s11227-018-2272-2
Publikováno v:
Journal of Computational Chemistry. 39:1192-1199
A microscopic expression of the pressure tensor using the fast multipole method (FMM) with periodic boundary conditions has been derived. The pressure tensor calculated using this expression has been compared with that obtained using the Ewald method
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::f6b0f00f0385df2656b68b7b708b01bb
https://doi.org/10.1002/jcc.25179
https://doi.org/10.1002/jcc.25179
Publikováno v:
Journal of Chemical Physics; 2017, Vol. 147 Issue 8, p1-8, 8p, 1 Color Photograph, 3 Diagrams, 8 Graphs
Publikováno v:
Journal of Chemical Physics; 2017, Vol. 147 Issue 3, p1-9, 9p, 1 Diagram, 2 Charts, 7 Graphs
Publikováno v:
Molecular Simulation. 43:1331-1337
We studied dynamic scaling law for the early stage domain growth in the micelle aggregation process of dispersed surfactant molecules in water for zwitterionic dodecyldimethylamine oxide (DDAO) and...
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::379d6aaba8381c58a0439aac2304f246
https://doi.org/10.1080/08927022.2017.1328557
https://doi.org/10.1080/08927022.2017.1328557
Publikováno v:
Journal of Computational Chemistry. 38:704-713
In molecular dynamics (MD) calculations, reduction in calculation time per MD loop is essential. A multiple time-step (MTS) integration algorithm, the RESPA (Tuckerman and Berne, J. Chem. Phys. 1992, 97, 1990-2001), enables reductions in calculation
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fde612bd9abc83f8390a0c4154f0810b
https://doi.org/10.1002/jcc.24731
https://doi.org/10.1002/jcc.24731