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Energy, Structures, and Response Properties with a Fully Coupled QM/AMOEBA/ddCOSMO Implementation
[Image: see text] We present the implementation of a fully coupled polarizable QM/MM/continuum model based on the AMOEBA polarizable force field and the domain decomposition implementation of the conductor-like screening model. Energies, response properties, and analytical gradients with respect to...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2021
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8444335/ https://www.ncbi.nlm.nih.gov/pubmed/34476941 http://dx.doi.org/10.1021/acs.jctc.1c00555 |
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author | Nottoli, Michele Nifosì, Riccardo Mennucci, Benedetta Lipparini, Filippo |
author_facet | Nottoli, Michele Nifosì, Riccardo Mennucci, Benedetta Lipparini, Filippo |
author_sort | Nottoli, Michele |
collection | PubMed |
description | [Image: see text] We present the implementation of a fully coupled polarizable QM/MM/continuum model based on the AMOEBA polarizable force field and the domain decomposition implementation of the conductor-like screening model. Energies, response properties, and analytical gradients with respect to both QM and MM nuclear positions are available, and a generic, atomistic cavity can be employed. The model is linear scaling in memory requirements and computational cost with respect to the number of classical atoms and is therefore suited to model large, complex systems. Using three variants of the green-fluorescent protein, we investigate the overall computational cost of such calculations and the effect of the continuum model on the convergence of the computed properties with respect to the size of the embedding. We also demonstrate the fundamental role of polarization effects by comparing polarizable and nonpolarizable embeddings to fully QM ones. |
format | Online Article Text |
id | pubmed-8444335 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-84443352021-09-20 Energy, Structures, and Response Properties with a Fully Coupled QM/AMOEBA/ddCOSMO Implementation Nottoli, Michele Nifosì, Riccardo Mennucci, Benedetta Lipparini, Filippo J Chem Theory Comput [Image: see text] We present the implementation of a fully coupled polarizable QM/MM/continuum model based on the AMOEBA polarizable force field and the domain decomposition implementation of the conductor-like screening model. Energies, response properties, and analytical gradients with respect to both QM and MM nuclear positions are available, and a generic, atomistic cavity can be employed. The model is linear scaling in memory requirements and computational cost with respect to the number of classical atoms and is therefore suited to model large, complex systems. Using three variants of the green-fluorescent protein, we investigate the overall computational cost of such calculations and the effect of the continuum model on the convergence of the computed properties with respect to the size of the embedding. We also demonstrate the fundamental role of polarization effects by comparing polarizable and nonpolarizable embeddings to fully QM ones. American Chemical Society 2021-09-03 2021-09-14 /pmc/articles/PMC8444335/ /pubmed/34476941 http://dx.doi.org/10.1021/acs.jctc.1c00555 Text en © 2021 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Nottoli, Michele Nifosì, Riccardo Mennucci, Benedetta Lipparini, Filippo Energy, Structures, and Response Properties with a Fully Coupled QM/AMOEBA/ddCOSMO Implementation |
title | Energy, Structures, and Response Properties with a
Fully Coupled QM/AMOEBA/ddCOSMO Implementation |
title_full | Energy, Structures, and Response Properties with a
Fully Coupled QM/AMOEBA/ddCOSMO Implementation |
title_fullStr | Energy, Structures, and Response Properties with a
Fully Coupled QM/AMOEBA/ddCOSMO Implementation |
title_full_unstemmed | Energy, Structures, and Response Properties with a
Fully Coupled QM/AMOEBA/ddCOSMO Implementation |
title_short | Energy, Structures, and Response Properties with a
Fully Coupled QM/AMOEBA/ddCOSMO Implementation |
title_sort | energy, structures, and response properties with a
fully coupled qm/amoeba/ddcosmo implementation |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8444335/ https://www.ncbi.nlm.nih.gov/pubmed/34476941 http://dx.doi.org/10.1021/acs.jctc.1c00555 |
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