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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...

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Autores principales: Peters, Laurens D. M., Kussmann, Jörg, Ochsenfeld, Christian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2020
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.
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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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