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Combining Graphics Processing Units, Simplified Time-Dependent Density Functional Theory, and Finite-Difference Couplings to Accelerate Nonadiabatic Molecular Dynamics
[Image: see text] Starting from our recently published implementation of nonadiabatic molecular dynamics (NAMD) on graphics processing units (GPUs), we explore further approaches to accelerate ab initio NAMD calculations at the time-dependent density functional theory (TDDFT) level of theory. We emp...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical
Society
2020
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7304892/ https://www.ncbi.nlm.nih.gov/pubmed/32374606 http://dx.doi.org/10.1021/acs.jpclett.0c00320 |
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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] Starting from our recently published implementation of nonadiabatic molecular dynamics (NAMD) on graphics processing units (GPUs), we explore further approaches to accelerate ab initio NAMD calculations at the time-dependent density functional theory (TDDFT) level of theory. We employ (1) the simplified TDDFT schemes of Grimme et al. and (2) the Hammes-Schiffer–Tully approach to obtain nonadiabatic couplings from finite-difference calculations. The resulting scheme delivers an accurate physical picture while virtually eliminating the two computationally most demanding steps of the algorithm. Combined with our GPU-based integral routines for SCF, TDDFT, and TDDFT derivative calculations, NAMD simulations of systems of a few hundreds of atoms at a reasonable time scale become accessible on a single compute node. To demonstrate this and to present a first, illustrative example, we perform TDDFT/MM-NAMD simulations of the rhodopsin protein. |
format | Online Article Text |
id | pubmed-7304892 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | American Chemical
Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-73048922020-06-22 Combining Graphics Processing Units, Simplified Time-Dependent Density Functional Theory, and Finite-Difference Couplings to Accelerate Nonadiabatic Molecular Dynamics Peters, Laurens D. M. Kussmann, Jörg Ochsenfeld, Christian J Phys Chem Lett [Image: see text] Starting from our recently published implementation of nonadiabatic molecular dynamics (NAMD) on graphics processing units (GPUs), we explore further approaches to accelerate ab initio NAMD calculations at the time-dependent density functional theory (TDDFT) level of theory. We employ (1) the simplified TDDFT schemes of Grimme et al. and (2) the Hammes-Schiffer–Tully approach to obtain nonadiabatic couplings from finite-difference calculations. The resulting scheme delivers an accurate physical picture while virtually eliminating the two computationally most demanding steps of the algorithm. Combined with our GPU-based integral routines for SCF, TDDFT, and TDDFT derivative calculations, NAMD simulations of systems of a few hundreds of atoms at a reasonable time scale become accessible on a single compute node. To demonstrate this and to present a first, illustrative example, we perform TDDFT/MM-NAMD simulations of the rhodopsin protein. American Chemical Society 2020-05-06 2020-05-21 /pmc/articles/PMC7304892/ /pubmed/32374606 http://dx.doi.org/10.1021/acs.jpclett.0c00320 Text en Copyright © 2020 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 Combining Graphics Processing Units, Simplified Time-Dependent Density Functional Theory, and Finite-Difference Couplings to Accelerate Nonadiabatic Molecular Dynamics |
title | Combining Graphics Processing Units, Simplified Time-Dependent
Density Functional Theory, and Finite-Difference Couplings to Accelerate
Nonadiabatic Molecular Dynamics |
title_full | Combining Graphics Processing Units, Simplified Time-Dependent
Density Functional Theory, and Finite-Difference Couplings to Accelerate
Nonadiabatic Molecular Dynamics |
title_fullStr | Combining Graphics Processing Units, Simplified Time-Dependent
Density Functional Theory, and Finite-Difference Couplings to Accelerate
Nonadiabatic Molecular Dynamics |
title_full_unstemmed | Combining Graphics Processing Units, Simplified Time-Dependent
Density Functional Theory, and Finite-Difference Couplings to Accelerate
Nonadiabatic Molecular Dynamics |
title_short | Combining Graphics Processing Units, Simplified Time-Dependent
Density Functional Theory, and Finite-Difference Couplings to Accelerate
Nonadiabatic Molecular Dynamics |
title_sort | combining graphics processing units, simplified time-dependent
density functional theory, and finite-difference couplings to accelerate
nonadiabatic molecular dynamics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7304892/ https://www.ncbi.nlm.nih.gov/pubmed/32374606 http://dx.doi.org/10.1021/acs.jpclett.0c00320 |
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