Adaptive QM/MM for Molecular Dynamics Simulations: 5. On the Energy-Conserved Permuted Adaptive-Partitioning Schemes

In combined quantum-mechanical/molecular-mechanical (QM/MM) dynamics simulations, the adaptive-partitioning (AP) schemes reclassify atoms on-the-fly as QM or MM in a smooth manner. This yields a mobile QM subsystem with contents that are continuously updated as needed. Here, we tailor the Hamiltonia...

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Autores principales: Duster, Adam W., Wang, Chun-Hung, Lin, Hai
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2018
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6225285/
https://www.ncbi.nlm.nih.gov/pubmed/30154373
http://dx.doi.org/10.3390/molecules23092170
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author Duster, Adam W.
Wang, Chun-Hung
Lin, Hai
author_facet Duster, Adam W.
Wang, Chun-Hung
Lin, Hai
author_sort Duster, Adam W.
collection PubMed
description In combined quantum-mechanical/molecular-mechanical (QM/MM) dynamics simulations, the adaptive-partitioning (AP) schemes reclassify atoms on-the-fly as QM or MM in a smooth manner. This yields a mobile QM subsystem with contents that are continuously updated as needed. Here, we tailor the Hamiltonian adaptive many-body correction (HAMBC) proposed by Boreboom et al. [J. Chem. Theory Comput. 2016, 12, 3441] to the permuted AP (PAP) scheme. The treatments lead to the HAMBC-PAP method (HPAP), which both conserves energy and produces accurate solvation structures in the test of “water-in-water” model system.
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spelling pubmed-62252852018-11-13 Adaptive QM/MM for Molecular Dynamics Simulations: 5. On the Energy-Conserved Permuted Adaptive-Partitioning Schemes Duster, Adam W. Wang, Chun-Hung Lin, Hai Molecules Article In combined quantum-mechanical/molecular-mechanical (QM/MM) dynamics simulations, the adaptive-partitioning (AP) schemes reclassify atoms on-the-fly as QM or MM in a smooth manner. This yields a mobile QM subsystem with contents that are continuously updated as needed. Here, we tailor the Hamiltonian adaptive many-body correction (HAMBC) proposed by Boreboom et al. [J. Chem. Theory Comput. 2016, 12, 3441] to the permuted AP (PAP) scheme. The treatments lead to the HAMBC-PAP method (HPAP), which both conserves energy and produces accurate solvation structures in the test of “water-in-water” model system. MDPI 2018-08-28 /pmc/articles/PMC6225285/ /pubmed/30154373 http://dx.doi.org/10.3390/molecules23092170 Text en © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Duster, Adam W.
Wang, Chun-Hung
Lin, Hai
Adaptive QM/MM for Molecular Dynamics Simulations: 5. On the Energy-Conserved Permuted Adaptive-Partitioning Schemes
title Adaptive QM/MM for Molecular Dynamics Simulations: 5. On the Energy-Conserved Permuted Adaptive-Partitioning Schemes
title_full Adaptive QM/MM for Molecular Dynamics Simulations: 5. On the Energy-Conserved Permuted Adaptive-Partitioning Schemes
title_fullStr Adaptive QM/MM for Molecular Dynamics Simulations: 5. On the Energy-Conserved Permuted Adaptive-Partitioning Schemes
title_full_unstemmed Adaptive QM/MM for Molecular Dynamics Simulations: 5. On the Energy-Conserved Permuted Adaptive-Partitioning Schemes
title_short Adaptive QM/MM for Molecular Dynamics Simulations: 5. On the Energy-Conserved Permuted Adaptive-Partitioning Schemes
title_sort adaptive qm/mm for molecular dynamics simulations: 5. on the energy-conserved permuted adaptive-partitioning schemes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6225285/
https://www.ncbi.nlm.nih.gov/pubmed/30154373
http://dx.doi.org/10.3390/molecules23092170
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AT linhai adaptiveqmmmformoleculardynamicssimulations5ontheenergyconservedpermutedadaptivepartitioningschemes

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