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231224s2016 xx |||||o 00| ||eng c |
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|a 10.1002/jcc.24497
|2 doi
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|a pubmed25n0883.xml
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|a (DE-627)NLM265121744
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|a (NLM)27718264
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|a DE-627
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|c DE-627
|e rakwb
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|a eng
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|a Nishizawa, Hiroaki
|e verfasserin
|4 aut
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|a Rapid QM/MM approach for biomolecular systems under periodic boundary conditions
|b Combination of the density-functional tight-binding theory and particle mesh Ewald method
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|c 2016
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|a Text
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|2 rdacontent
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|a ƒaComputermedien
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|2 rdamedia
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|a ƒa Online-Ressource
|b cr
|2 rdacarrier
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|a Date Completed 19.07.2018
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|a Date Revised 19.07.2018
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|a published: Print-Electronic
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|a Citation Status PubMed-not-MEDLINE
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|a © 2016 Wiley Periodicals, Inc.
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|a A quantum mechanical/molecular mechanical (QM/MM) approach based on the density-functional tight-binding (DFTB) theory is a useful tool for analyzing chemical reaction systems in detail. In this study, an efficient QM/MM method is developed by the combination of the DFTB/MM and particle mesh Ewald (PME) methods. Because the Fock matrix, which is required in the DFTB calculation, is analytically obtained by the PME method, the Coulomb energy is accurately and rapidly computed. For assessing the performance of this method, DFTB/MM calculations and molecular dynamics simulation are conducted for a system consisting of two amyloid-β(1-16) peptides and a zinc ion in explicit water under periodic boundary conditions. As compared with that of the conventional Ewald summation method, the computational cost of the Coulomb energy by utilizing the present approach is drastically reduced, i.e., 166.5 times faster. Furthermore, the deviation of the electronic energy is less than 10-6 Eh. © 2016 Wiley Periodicals, Inc
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|a Journal Article
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|a Research Support, Non-U.S. Gov't
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|a biomolecule
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|a density-functional tight-binding theory
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|a molecular dynamics
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|a particle mesh Ewald method
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| 650 |
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|a periodic boundary condition
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| 650 |
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|a quantum mechanical/molecular mechanical treatment
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|a Okumura, Hisashi
|e verfasserin
|4 aut
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| 773 |
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|i Enthalten in
|t Journal of computational chemistry
|d 1984
|g 37(2016), 31 vom: 05. Dez., Seite 2701-2711
|w (DE-627)NLM098138448
|x 1096-987X
|7 nnns
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| 773 |
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|g volume:37
|g year:2016
|g number:31
|g day:05
|g month:12
|g pages:2701-2711
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|u http://dx.doi.org/10.1002/jcc.24497
|3 Volltext
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