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Nonadiabatic Molecular Dynamics on Graphics Processing Units: Performance and Application to Rotary Molecular Motors
[Image: see text] Nonadiabatic molecular dynamics (NAMD) simulations of molecular systems require the efficient evaluation of excited-state properties, such as energies, gradients, and nonadiabatic coupling vectors. Here, we investigate the use of graphics processing units (GPUs) in addition to cent...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2019
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6909237/ https://www.ncbi.nlm.nih.gov/pubmed/31763834 http://dx.doi.org/10.1021/acs.jctc.9b00859 |
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author | Peters, Laurens D. M. Kussmann, Jörg Ochsenfeld, Christian |
author_facet | Peters, Laurens D. M. Kussmann, Jörg Ochsenfeld, Christian |
author_sort | Peters, Laurens D. M. |
collection | PubMed |
description | [Image: see text] Nonadiabatic molecular dynamics (NAMD) simulations of molecular systems require the efficient evaluation of excited-state properties, such as energies, gradients, and nonadiabatic coupling vectors. Here, we investigate the use of graphics processing units (GPUs) in addition to central processing units (CPUs) to efficiently calculate these properties at the time-dependent density functional theory (TDDFT) level of theory. Our implementation in the FermiONs++ program package uses the J-engine and a preselective screening procedure for the calculation of Coulomb and exchange kernels, respectively. We observe good speed-ups for small and large molecular systems (comparable to those observed in ground-state calculations) and reduced (down to sublinear) scaling behavior with respect to the system size (depending on the spatial locality of the investigated excitation). As a first illustrative application, we present efficient NAMD simulations of a series of newly designed light-driven rotary molecular motors and compare their S(1) lifetimes. Although all four rotors show different S(1) excitation energies, their ability to rotate upon excitation is conserved, making the series an interesting starting point for rotary molecular motors with tunable excitation energies. |
format | Online Article Text |
id | pubmed-6909237 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-69092372019-12-19 Nonadiabatic Molecular Dynamics on Graphics Processing Units: Performance and Application to Rotary Molecular Motors Peters, Laurens D. M. Kussmann, Jörg Ochsenfeld, Christian J Chem Theory Comput [Image: see text] Nonadiabatic molecular dynamics (NAMD) simulations of molecular systems require the efficient evaluation of excited-state properties, such as energies, gradients, and nonadiabatic coupling vectors. Here, we investigate the use of graphics processing units (GPUs) in addition to central processing units (CPUs) to efficiently calculate these properties at the time-dependent density functional theory (TDDFT) level of theory. Our implementation in the FermiONs++ program package uses the J-engine and a preselective screening procedure for the calculation of Coulomb and exchange kernels, respectively. We observe good speed-ups for small and large molecular systems (comparable to those observed in ground-state calculations) and reduced (down to sublinear) scaling behavior with respect to the system size (depending on the spatial locality of the investigated excitation). As a first illustrative application, we present efficient NAMD simulations of a series of newly designed light-driven rotary molecular motors and compare their S(1) lifetimes. Although all four rotors show different S(1) excitation energies, their ability to rotate upon excitation is conserved, making the series an interesting starting point for rotary molecular motors with tunable excitation energies. American Chemical Society 2019-11-25 2019-12-10 /pmc/articles/PMC6909237/ /pubmed/31763834 http://dx.doi.org/10.1021/acs.jctc.9b00859 Text en Copyright © 2019 American Chemical Society This is an open access article published under a Creative Commons Attribution (CC-BY) License (http://pubs.acs.org/page/policy/authorchoice_ccby_termsofuse.html) , which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited. |
spellingShingle | Peters, Laurens D. M. Kussmann, Jörg Ochsenfeld, Christian Nonadiabatic Molecular Dynamics on Graphics Processing Units: Performance and Application to Rotary Molecular Motors |
title | Nonadiabatic Molecular
Dynamics on Graphics Processing
Units: Performance and Application to Rotary Molecular Motors |
title_full | Nonadiabatic Molecular
Dynamics on Graphics Processing
Units: Performance and Application to Rotary Molecular Motors |
title_fullStr | Nonadiabatic Molecular
Dynamics on Graphics Processing
Units: Performance and Application to Rotary Molecular Motors |
title_full_unstemmed | Nonadiabatic Molecular
Dynamics on Graphics Processing
Units: Performance and Application to Rotary Molecular Motors |
title_short | Nonadiabatic Molecular
Dynamics on Graphics Processing
Units: Performance and Application to Rotary Molecular Motors |
title_sort | nonadiabatic molecular
dynamics on graphics processing
units: performance and application to rotary molecular motors |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6909237/ https://www.ncbi.nlm.nih.gov/pubmed/31763834 http://dx.doi.org/10.1021/acs.jctc.9b00859 |
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