Journal
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
Volume 9, Issue 7, Pages 3201-3209Publisher
AMER CHEMICAL SOC
DOI: 10.1021/ct400203a
Keywords
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Funding
- Next Generation Super Computing Project
- Nanoscience Program
- TCCI/CMSI in the Strategic Programs for Innovative Research, MEXT, Japan
- Grants-in-Aid for Scientific Research [23550027] Funding Source: KAKEN
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Our new molecular dynamics (MD) simulation program, MODYLAS, is a general-purpose program appropriate for very large physical, chemical, and biological systems. It is equipped with most standard MD techniques. Long-range forces are evaluated rigorously by the fast multipole method (FMM) without using the fast Fourier transform (FFT). Several new methods have also been developed for extremely fine-grained parallelism of the MD calculation. The virtually buffering-free methods for communications and arithmetic Operations, the minimal communication latency algorithm, and the parallel bucket-relay communication algorithm for the upper-level multipole moments in the FMM realize excellent scalability. The methods for blockwise arithmetic operations avoid data reload, attaining very small cache miss rates. Benchmark tests for MODYLAS using 65 536 nodes of the K-computer showed that the overall calculation time per MD step including communications is as short as about 5 ins for a 10 million-atom system; that is, 35 ns of simulation time can be computed per day. The program enables investigations of large-scale real systems such as viruses, liposomes, assemblies of proteins and micelles, and polymers.
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