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PyMM: An Open-Source Python Program for QM/MM Simulations Based on the Perturbed Matrix Method
[Image: see text] Quantum mechanical/molecular mechanics (QM/MM) methods are important tools in molecular modeling as they are able to couple an extended phase space sampling with an accurate description of the electronic properties of the system. Here, we describe a Python software package, called...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9835827/ https://www.ncbi.nlm.nih.gov/pubmed/36378163 http://dx.doi.org/10.1021/acs.jctc.2c00767 |
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author | Chen, Cheng Giuseppe Nardi, Alessandro Nicola Amadei, Andrea D’Abramo, Marco |
author_facet | Chen, Cheng Giuseppe Nardi, Alessandro Nicola Amadei, Andrea D’Abramo, Marco |
author_sort | Chen, Cheng Giuseppe |
collection | PubMed |
description | [Image: see text] Quantum mechanical/molecular mechanics (QM/MM) methods are important tools in molecular modeling as they are able to couple an extended phase space sampling with an accurate description of the electronic properties of the system. Here, we describe a Python software package, called PyMM, which has been developed to apply a QM/MM approach, the perturbed matrix method, in a simple and efficient way. PyMM requires a classical atomic trajectory of the whole system and a set of unperturbed electronic properties of the ground and electronic excited states. The software output includes a set of the most common perturbed properties, such as the electronic excitation energies and the transitions dipole moments, as well as the eigenvectors describing the perturbed electronic states, which can be then used to estimate whatever electronic property. The software is composed of a simple and complete command-line interface, a set of internal input validation, and three main analyses focusing on (i) the perturbed eigenvector behavior, (ii) the calculation of the electronic absorption spectrum, and (iii) the estimation of the free energy differences along a reaction coordinate. |
format | Online Article Text |
id | pubmed-9835827 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-98358272023-01-13 PyMM: An Open-Source Python Program for QM/MM Simulations Based on the Perturbed Matrix Method Chen, Cheng Giuseppe Nardi, Alessandro Nicola Amadei, Andrea D’Abramo, Marco J Chem Theory Comput [Image: see text] Quantum mechanical/molecular mechanics (QM/MM) methods are important tools in molecular modeling as they are able to couple an extended phase space sampling with an accurate description of the electronic properties of the system. Here, we describe a Python software package, called PyMM, which has been developed to apply a QM/MM approach, the perturbed matrix method, in a simple and efficient way. PyMM requires a classical atomic trajectory of the whole system and a set of unperturbed electronic properties of the ground and electronic excited states. The software output includes a set of the most common perturbed properties, such as the electronic excitation energies and the transitions dipole moments, as well as the eigenvectors describing the perturbed electronic states, which can be then used to estimate whatever electronic property. The software is composed of a simple and complete command-line interface, a set of internal input validation, and three main analyses focusing on (i) the perturbed eigenvector behavior, (ii) the calculation of the electronic absorption spectrum, and (iii) the estimation of the free energy differences along a reaction coordinate. American Chemical Society 2022-11-15 /pmc/articles/PMC9835827/ /pubmed/36378163 http://dx.doi.org/10.1021/acs.jctc.2c00767 Text en © 2022 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 | Chen, Cheng Giuseppe Nardi, Alessandro Nicola Amadei, Andrea D’Abramo, Marco PyMM: An Open-Source Python Program for QM/MM Simulations Based on the Perturbed Matrix Method |
title | PyMM: An Open-Source
Python Program for QM/MM Simulations
Based on the Perturbed Matrix Method |
title_full | PyMM: An Open-Source
Python Program for QM/MM Simulations
Based on the Perturbed Matrix Method |
title_fullStr | PyMM: An Open-Source
Python Program for QM/MM Simulations
Based on the Perturbed Matrix Method |
title_full_unstemmed | PyMM: An Open-Source
Python Program for QM/MM Simulations
Based on the Perturbed Matrix Method |
title_short | PyMM: An Open-Source
Python Program for QM/MM Simulations
Based on the Perturbed Matrix Method |
title_sort | pymm: an open-source
python program for qm/mm simulations
based on the perturbed matrix method |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9835827/ https://www.ncbi.nlm.nih.gov/pubmed/36378163 http://dx.doi.org/10.1021/acs.jctc.2c00767 |
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