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231224s2015 xx |||||o 00| ||eng c |
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|a 10.1002/jcc.23839
|2 doi
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|a pubmed25n0819.xml
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|a (DE-627)NLM245930744
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|a (NLM)25649827
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|a DE-627
|b ger
|c DE-627
|e rakwb
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|a eng
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| 100 |
1 |
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|a Mones, Letif
|e verfasserin
|4 aut
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|a The adaptive buffered force QM/MM method in the CP2K and AMBER software packages
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|c 2015
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|a Text
|b txt
|2 rdacontent
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|a ƒaComputermedien
|b c
|2 rdamedia
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|a ƒa Online-Ressource
|b cr
|2 rdacarrier
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|a Date Completed 28.10.2015
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|a Date Revised 13.11.2018
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|a published: Print-Electronic
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|a Citation Status MEDLINE
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|a © 2015 Wiley Periodicals, Inc.
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|a The implementation and validation of the adaptive buffered force (AdBF) quantum-mechanics/molecular-mechanics (QM/MM) method in two popular packages, CP2K and AMBER are presented. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM-MM interface errors by discarding forces near the boundary according to the buffered force-mixing approach. New adaptive thermostats, needed by force-mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl-phosphate hydrolysis using various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the AdBF QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reproducing the correct energetics in all cases. Adaptive unbuffered force-mixing and adaptive conventional QM/MM methods also provide reasonable results for some systems, but are more likely to suffer from instabilities and inaccuracies
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|a Journal Article
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|a Research Support, N.I.H., Extramural
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|a Research Support, Non-U.S. Gov't
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| 650 |
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|a Research Support, U.S. Gov't, Non-P.H.S.
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| 650 |
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|a adaptive quantum-mechanics/molecular-mechanics
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| 650 |
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|a force-mixing
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| 650 |
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4 |
|a multiscale
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| 650 |
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|a quantum-mechanics/molecular-mechanics
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| 650 |
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|a Organophosphorus Compounds
|2 NLM
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| 650 |
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|a Water
|2 NLM
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| 650 |
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|a 059QF0KO0R
|2 NLM
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| 650 |
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|a dimethyl phosphate
|2 NLM
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| 650 |
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7 |
|a HI4K2C9UEI
|2 NLM
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| 650 |
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|a Zinc
|2 NLM
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| 650 |
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|a J41CSQ7QDS
|2 NLM
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| 700 |
1 |
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|a Jones, Andrew
|e verfasserin
|4 aut
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| 700 |
1 |
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|a Götz, Andreas W
|e verfasserin
|4 aut
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| 700 |
1 |
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|a Laino, Teodoro
|e verfasserin
|4 aut
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| 700 |
1 |
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|a Walker, Ross C
|e verfasserin
|4 aut
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| 700 |
1 |
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|a Leimkuhler, Ben
|e verfasserin
|4 aut
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| 700 |
1 |
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|a Csányi, Gábor
|e verfasserin
|4 aut
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| 700 |
1 |
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|a Bernstein, Noam
|e verfasserin
|4 aut
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| 773 |
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|i Enthalten in
|t Journal of computational chemistry
|d 1984
|g 36(2015), 9 vom: 05. Apr., Seite 633-48
|w (DE-627)NLM098138448
|x 1096-987X
|7 nnns
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| 773 |
1 |
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|g volume:36
|g year:2015
|g number:9
|g day:05
|g month:04
|g pages:633-48
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| 856 |
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|u http://dx.doi.org/10.1002/jcc.23839
|3 Volltext
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