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Data driven inference for the repulsive exponent of the Lennard-Jones potential in molecular dynamics simulations
The Lennard-Jones (LJ) potential is a cornerstone of Molecular Dynamics (MD) simulations and among the most widely used computational kernels in science. The LJ potential models atomistic attraction and repulsion with century old prescribed parameters (q = 6, p = 12, respectively), originally relate...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5707428/ https://www.ncbi.nlm.nih.gov/pubmed/29185461 http://dx.doi.org/10.1038/s41598-017-16314-4 |
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author | Kulakova, Lina Arampatzis, Georgios Angelikopoulos, Panagiotis Hadjidoukas, Panagiotis Papadimitriou, Costas Koumoutsakos, Petros |
author_facet | Kulakova, Lina Arampatzis, Georgios Angelikopoulos, Panagiotis Hadjidoukas, Panagiotis Papadimitriou, Costas Koumoutsakos, Petros |
author_sort | Kulakova, Lina |
collection | PubMed |
description | The Lennard-Jones (LJ) potential is a cornerstone of Molecular Dynamics (MD) simulations and among the most widely used computational kernels in science. The LJ potential models atomistic attraction and repulsion with century old prescribed parameters (q = 6, p = 12, respectively), originally related by a factor of two for simplicity of calculations. We propose the inference of the repulsion exponent through Hierarchical Bayesian uncertainty quantification We use experimental data of the radial distribution function and dimer interaction energies from quantum mechanics simulations. We find that the repulsion exponent p ≈ 6.5 provides an excellent fit for the experimental data of liquid argon, for a range of thermodynamic conditions, as well as for saturated argon vapour. Calibration using the quantum simulation data did not provide a good fit in these cases. However, values p ≈ 12.7 obtained by dimer quantum simulations are preferred for the argon gas while lower values are promoted by experimental data. These results show that the proposed LJ 6-p potential applies to a wider range of thermodynamic conditions, than the classical LJ 6-12 potential. We suggest that calibration of the repulsive exponent in the LJ potential widens the range of applicability and accuracy of MD simulations. |
format | Online Article Text |
id | pubmed-5707428 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-57074282017-12-06 Data driven inference for the repulsive exponent of the Lennard-Jones potential in molecular dynamics simulations Kulakova, Lina Arampatzis, Georgios Angelikopoulos, Panagiotis Hadjidoukas, Panagiotis Papadimitriou, Costas Koumoutsakos, Petros Sci Rep Article The Lennard-Jones (LJ) potential is a cornerstone of Molecular Dynamics (MD) simulations and among the most widely used computational kernels in science. The LJ potential models atomistic attraction and repulsion with century old prescribed parameters (q = 6, p = 12, respectively), originally related by a factor of two for simplicity of calculations. We propose the inference of the repulsion exponent through Hierarchical Bayesian uncertainty quantification We use experimental data of the radial distribution function and dimer interaction energies from quantum mechanics simulations. We find that the repulsion exponent p ≈ 6.5 provides an excellent fit for the experimental data of liquid argon, for a range of thermodynamic conditions, as well as for saturated argon vapour. Calibration using the quantum simulation data did not provide a good fit in these cases. However, values p ≈ 12.7 obtained by dimer quantum simulations are preferred for the argon gas while lower values are promoted by experimental data. These results show that the proposed LJ 6-p potential applies to a wider range of thermodynamic conditions, than the classical LJ 6-12 potential. We suggest that calibration of the repulsive exponent in the LJ potential widens the range of applicability and accuracy of MD simulations. Nature Publishing Group UK 2017-11-29 /pmc/articles/PMC5707428/ /pubmed/29185461 http://dx.doi.org/10.1038/s41598-017-16314-4 Text en © The Author(s) 2017 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Kulakova, Lina Arampatzis, Georgios Angelikopoulos, Panagiotis Hadjidoukas, Panagiotis Papadimitriou, Costas Koumoutsakos, Petros Data driven inference for the repulsive exponent of the Lennard-Jones potential in molecular dynamics simulations |
title | Data driven inference for the repulsive exponent of the Lennard-Jones potential in molecular dynamics simulations |
title_full | Data driven inference for the repulsive exponent of the Lennard-Jones potential in molecular dynamics simulations |
title_fullStr | Data driven inference for the repulsive exponent of the Lennard-Jones potential in molecular dynamics simulations |
title_full_unstemmed | Data driven inference for the repulsive exponent of the Lennard-Jones potential in molecular dynamics simulations |
title_short | Data driven inference for the repulsive exponent of the Lennard-Jones potential in molecular dynamics simulations |
title_sort | data driven inference for the repulsive exponent of the lennard-jones potential in molecular dynamics simulations |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5707428/ https://www.ncbi.nlm.nih.gov/pubmed/29185461 http://dx.doi.org/10.1038/s41598-017-16314-4 |
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