Development of a new density fuctional method for large molecules
| Project/Area Number |
11166252
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| Research Category |
Grant-in-Aid for Scientific Research on Priority Areas (A)
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| Allocation Type | Single-year Grants |
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| Review Section |
Science and Engineering
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| Research Institution | Kyushu Institute of Technology |
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Principal Investigator |
SATO Fumitoshi Faculty of computer Science and systems Engineerng, research associate, 情報工学部, 助手 (00235392)
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| Project Period (FY) |
1999 – 2001
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| Project Status |
Completed (Fiscal Year 2001)
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| Budget Amount *help |
¥3,500,000 (Direct Cost: ¥3,500,000)
Fiscal Year 1999: ¥3,500,000 (Direct Cost: ¥3,500,000)
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| Keywords | protein / density functional method / object-oriented / all-electron calculation / large molecule / parallel computing / cytochrome c / scenario editor / 大規模計算 / 収束法 / BDS-I / 並列化 |
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| Research Abstract |
The density functional (DF) method based on the Kohn-Sham (KS) equation is a powerful tool for studying the properties of molecular systems. The advantage of the method is that one can include die election correlation effect, while its computational task is the same order of that in the ab initio Hartree-Fock (HF) method From this point of view, the DF method is well suited for calculations on metal-containing large molecular systems such as hemoproteins. We have developed the molecular orbital (MO) program ProteinDF based on the Kohn-Sham-Roothaan (KSR) equation with Gaussian-type orbitals, and achieved an all-electron calculation on horse heart cytochrome c (cyt c) which is a typical hemoprotein consisting of 104 residues and one c-type heme. It is the first all-electron calculation on a metalloproteim. The number of atoms, electrons, orbitals and auxiliary functions in the calculation on cyt c were 1738, 6586, 9600 and 17578, respectively. There are a lot of scenarios in the convergence process of all-electron calculations of proteins. To assist users in scheduling of the process, we have developed a graphical user interface called "scenario editor". This system automatically proposes a convergence scenario for a user and allows him to modify it in windows with a mouse on personal computers. The scenario editor will open the way for both beginner and expert users to calculate protein all-electron wavefunctions.
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Report
(2 results)
Research Products
(15 results)
