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Andoh Y, Ichikawa SI, Sakashita T, Fujimoto K, Yoshii N, Nagai T, Tang Z, Okazaki S. An exa-scale high-performance molecular dynamics simulation program: MODYLAS. J Chem Phys 2023; 158:2890480. [PMID: 37184018 DOI: 10.1063/5.0144361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 04/25/2023] [Indexed: 05/16/2023] Open
Abstract
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 instruction, multiple data (SIMD) processing, and on-cache arithmetic operations. The system's performance deteriorated only slightly, even under high parallelization. In particular, a newly developed minimum transferred data method, requiring a significantly lower amount of data transfer compared to conventional communications, showed significantly high performance. The coordinates and forces of 101 810 176 atoms and the multipole coefficients of the subcells could be distributed to the 32 768 nodes (1 572 864 cores) in 2.3 ms during one MD step calculation. The SIMD effective instruction rates for floating-point arithmetic operations in direct force and fast multipole method (FMM) calculations measured on Fugaku were 78.7% and 31.5%, respectively. The development of a data reuse algorithm enhanced the on-cache processing; the cache miss rate for direct force and FMM calculations was only 2.74% and 1.43%, respectively, on the L1 cache and 0.08% and 0.60%, respectively, on the L2 cache. The modified MODYLAS could complete one MD single time-step calculation within 8.5 ms for the aforementioned large system. Additionally, the program contains numerous functions for material research that enable free energy calculations, along with the generation of various ensembles and molecular constraints.
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Affiliation(s)
- Yoshimichi Andoh
- National Institute for Materials Science (NIMS), 1-2-1, Sengen, Tsukuba, Ibaraki 305-0047, Japan
| | - Shin-Ichi Ichikawa
- Computational Science Division, Technical Computing Business Unit, Fujitsu Limited, Chiba, Japan
| | - Tatsuya Sakashita
- Center for Quantum Information and Quantum Biology, Osaka University, 1-2, Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Kazushi Fujimoto
- Department of Materials Chemistry, Nagoya University, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| | - Noriyuki Yoshii
- Center for Computational Science, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Tetsuro Nagai
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1, Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| | - Zhiye Tang
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, National Institutes of Natural Sciences, 38, Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Susumu Okazaki
- Department of Advanced Materials Science, The University of Tokyo, 5-1-5, Kashiwa-no-ha, Kashiwa, Chiba 277-0871, Japan
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Lynch DL, Pavlova A, Fan Z, Gumbart JC. Understanding Virus Structure and Dynamics through Molecular Simulations. J Chem Theory Comput 2023. [PMID: 37192279 DOI: 10.1021/acs.jctc.3c00116] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Viral outbreaks remain a serious threat to human and animal populations and motivate the continued development of antiviral drugs and vaccines, which in turn benefits from a detailed understanding of both viral structure and dynamics. While great strides have been made in characterizing these systems experimentally, molecular simulations have proven to be an essential, complementary approach. In this work, we review the contributions of molecular simulations to the understanding of viral structure, functional dynamics, and processes related to the viral life cycle. Approaches ranging from coarse-grained to all-atom representations are discussed, including current efforts at modeling complete viral systems. Overall, this review demonstrates that computational virology plays an essential role in understanding these systems.
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Affiliation(s)
- Diane L Lynch
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Zixing Fan
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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Nagai T, Yoshimori A, Okazaki S. Dynamic Monte Carlo calculation generating particle trajectories that satisfy the diffusion equation for heterogeneous systems with a position-dependent diffusion coefficient and free energy. J Chem Phys 2022; 156:154506. [PMID: 35459306 DOI: 10.1063/5.0086949] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A series of new Monte Carlo (MC) transition probabilities was investigated that could produce molecular trajectories statistically satisfying the diffusion equation with a position-dependent diffusion coefficient and potential energy. The MC trajectories were compared with the numerical solution of the diffusion equation by calculating the time evolution of the probability distribution and the mean first passage time, which exhibited excellent agreement. The method is powerful when investigating, for example, the long-distance and long-time global transportation of a molecule in heterogeneous systems by coarse-graining them into one-particle diffusive molecular motion with a position-dependent diffusion coefficient and free energy. The method can also be applied to many-particle dynamics.
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Affiliation(s)
- Tetsuro Nagai
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8561, Japan
| | - Akira Yoshimori
- Department of Physics, Niigata University, Niigata 950-2181, Japan
| | - Susumu Okazaki
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8561, Japan
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