Chemical Reactivity and Spectroscopy Explored From QM/MM Molecular Dynamics Simulations Using the LIO Code
In this work we present the current advances in the development and the applications of LIO, a lab-made code designed for density functional theory calculations in graphical processing units (GPU), that can be coupled with different classical molecular dynamics engines. This code has been thoroughly...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-03-01
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| Series: | Frontiers in Chemistry |
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| Online Access: | http://journal.frontiersin.org/article/10.3389/fchem.2018.00070/full |
| _version_ | 1818194052927979520 |
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| author | Juan P. Marcolongo Ari Zeida Ari Zeida Jonathan A. Semelak Nicolás O. Foglia Uriel N. Morzan Dario A. Estrin Mariano C. González Lebrero Damián A. Scherlis |
| author_facet | Juan P. Marcolongo Ari Zeida Ari Zeida Jonathan A. Semelak Nicolás O. Foglia Uriel N. Morzan Dario A. Estrin Mariano C. González Lebrero Damián A. Scherlis |
| author_sort | Juan P. Marcolongo |
| collection | DOAJ |
| description | In this work we present the current advances in the development and the applications of LIO, a lab-made code designed for density functional theory calculations in graphical processing units (GPU), that can be coupled with different classical molecular dynamics engines. This code has been thoroughly optimized to perform efficient molecular dynamics simulations at the QM/MM DFT level, allowing for an exhaustive sampling of the configurational space. Selected examples are presented for the description of chemical reactivity in terms of free energy profiles, and also for the computation of optical properties, such as vibrational and electronic spectra in solvent and protein environments. |
| first_indexed | 2024-12-12T00:56:10Z |
| format | Article |
| id | doaj.art-1928a6f3e2874769910288f5cdfb7221 |
| institution | Directory Open Access Journal |
| issn | 2296-2646 |
| language | English |
| last_indexed | 2024-12-12T00:56:10Z |
| publishDate | 2018-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Chemistry |
| spelling | doaj.art-1928a6f3e2874769910288f5cdfb72212022-12-22T00:43:53ZengFrontiers Media S.A.Frontiers in Chemistry2296-26462018-03-01610.3389/fchem.2018.00070359801Chemical Reactivity and Spectroscopy Explored From QM/MM Molecular Dynamics Simulations Using the LIO CodeJuan P. Marcolongo0Ari Zeida1Ari Zeida2Jonathan A. Semelak3Nicolás O. Foglia4Uriel N. Morzan5Dario A. Estrin6Mariano C. González Lebrero7Damián A. Scherlis8DQIAyQF, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, ArgentinaDQIAyQF, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, ArgentinaDepartamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, UruguayDQIAyQF, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, ArgentinaDQIAyQF, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, ArgentinaDQIAyQF, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, ArgentinaDQIAyQF, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, ArgentinaDQIAyQF, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, ArgentinaDQIAyQF, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, ArgentinaIn this work we present the current advances in the development and the applications of LIO, a lab-made code designed for density functional theory calculations in graphical processing units (GPU), that can be coupled with different classical molecular dynamics engines. This code has been thoroughly optimized to perform efficient molecular dynamics simulations at the QM/MM DFT level, allowing for an exhaustive sampling of the configurational space. Selected examples are presented for the description of chemical reactivity in terms of free energy profiles, and also for the computation of optical properties, such as vibrational and electronic spectra in solvent and protein environments.http://journal.frontiersin.org/article/10.3389/fchem.2018.00070/fullQM/MMDFTGPUfree energyTDDFT |
| spellingShingle | Juan P. Marcolongo Ari Zeida Ari Zeida Jonathan A. Semelak Nicolás O. Foglia Uriel N. Morzan Dario A. Estrin Mariano C. González Lebrero Damián A. Scherlis Chemical Reactivity and Spectroscopy Explored From QM/MM Molecular Dynamics Simulations Using the LIO Code Frontiers in Chemistry QM/MM DFT GPU free energy TDDFT |
| title | Chemical Reactivity and Spectroscopy Explored From QM/MM Molecular Dynamics Simulations Using the LIO Code |
| title_full | Chemical Reactivity and Spectroscopy Explored From QM/MM Molecular Dynamics Simulations Using the LIO Code |
| title_fullStr | Chemical Reactivity and Spectroscopy Explored From QM/MM Molecular Dynamics Simulations Using the LIO Code |
| title_full_unstemmed | Chemical Reactivity and Spectroscopy Explored From QM/MM Molecular Dynamics Simulations Using the LIO Code |
| title_short | Chemical Reactivity and Spectroscopy Explored From QM/MM Molecular Dynamics Simulations Using the LIO Code |
| title_sort | chemical reactivity and spectroscopy explored from qm mm molecular dynamics simulations using the lio code |
| topic | QM/MM DFT GPU free energy TDDFT |
| url | http://journal.frontiersin.org/article/10.3389/fchem.2018.00070/full |
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