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The adaptive buffered force QM/MM method in the CP2K and AMBER software packages
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 th...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BlackWell Publishing Ltd
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4351341/ https://www.ncbi.nlm.nih.gov/pubmed/25649827 http://dx.doi.org/10.1002/jcc.23839 |
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author | Mones, Letif Jones, Andrew Götz, Andreas W Laino, Teodoro Walker, Ross C Leimkuhler, Ben Csányi, Gábor Bernstein, Noam |
author_facet | Mones, Letif Jones, Andrew Götz, Andreas W Laino, Teodoro Walker, Ross C Leimkuhler, Ben Csányi, Gábor Bernstein, Noam |
author_sort | Mones, Letif |
collection | PubMed |
description | 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. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. |
format | Online Article Text |
id | pubmed-4351341 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | BlackWell Publishing Ltd |
record_format | MEDLINE/PubMed |
spelling | pubmed-43513412015-07-31 The adaptive buffered force QM/MM method in the CP2K and AMBER software packages Mones, Letif Jones, Andrew Götz, Andreas W Laino, Teodoro Walker, Ross C Leimkuhler, Ben Csányi, Gábor Bernstein, Noam J Comput Chem Full Papers 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. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. BlackWell Publishing Ltd 2015-04-15 2015-02-03 /pmc/articles/PMC4351341/ /pubmed/25649827 http://dx.doi.org/10.1002/jcc.23839 Text en © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. http://creativecommons.org/licenses/by/4.0/ This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Full Papers Mones, Letif Jones, Andrew Götz, Andreas W Laino, Teodoro Walker, Ross C Leimkuhler, Ben Csányi, Gábor Bernstein, Noam The adaptive buffered force QM/MM method in the CP2K and AMBER software packages |
title | The adaptive buffered force QM/MM method in the CP2K and AMBER software packages |
title_full | The adaptive buffered force QM/MM method in the CP2K and AMBER software packages |
title_fullStr | The adaptive buffered force QM/MM method in the CP2K and AMBER software packages |
title_full_unstemmed | The adaptive buffered force QM/MM method in the CP2K and AMBER software packages |
title_short | The adaptive buffered force QM/MM method in the CP2K and AMBER software packages |
title_sort | adaptive buffered force qm/mm method in the cp2k and amber software packages |
topic | Full Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4351341/ https://www.ncbi.nlm.nih.gov/pubmed/25649827 http://dx.doi.org/10.1002/jcc.23839 |
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