期刊
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
卷 10, 期 11, 页码 4801-4812出版社
AMER CHEMICAL SOC
DOI: 10.1021/ct500489d
关键词
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资金
- Japan Society for Promotion of Science for Young Scientists [DC1]
- L-Daigakuin program
- Next Generation Super Computing Project, Nanoscience Program (MEXT, Japan)
- Computational Materials Science Initiative (CMSI, Japan)
- Grants-in-Aid for Scientific Research [12J04986, 26410013] Funding Source: KAKEN
We developed the energy and its gradient for the self-consistent-charge density-functional tight-binding (DFTB) method, combined with the fragment molecular orbital (FMO) approach, FMO-DFTB, including an optional a posteriori treatment for dispersion interaction, and evaluated its accuracy as well as computational efficiency for a set of representative systems: polypeptides, a DNA segment, and a small protein. The error in the total energy of FMO-DFTB versus full SCC-DFTB was below 1 kcal/mol for the polyalanine system consisting of about 2000 atoms partitioned into fragments containing 2 residues, and the optimized structures had root-mean-square deviations below 0.1 angstrom. The scaling of FMO-DFTB with the system size N is only marginally larger than linear [O(N-1.2) in the worst case]. A parallelization efficiency of 94% was achieved using 128 CPU cores, and we demonstrate the applicability of FMO-DFTB for systems containing more than one million atoms by performing a geometry optimization of a fullerite cluster.
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