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Virtual-Wall Model for Molecular Dynamics Simulation
A large number of molecules are usually required to model atomic walls in molecular dynamics simulations. A virtual-wall model is proposed in this study to describe fluid-wall molecular interactions, for reducing the computational time. The infinite repetition of unit cell structures within the atom...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6274448/ https://www.ncbi.nlm.nih.gov/pubmed/27941688 http://dx.doi.org/10.3390/molecules21121678 |
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author | Qian, Lijuan Tu, Chengxu Bao, Fubing Zhang, Yonghao |
author_facet | Qian, Lijuan Tu, Chengxu Bao, Fubing Zhang, Yonghao |
author_sort | Qian, Lijuan |
collection | PubMed |
description | A large number of molecules are usually required to model atomic walls in molecular dynamics simulations. A virtual-wall model is proposed in this study to describe fluid-wall molecular interactions, for reducing the computational time. The infinite repetition of unit cell structures within the atomic wall causes the periodicity of the force acting on a fluid molecule from the wall molecules. This force is first calculated and then stored in the memory. A fluid molecule appearing in the wall force field is subjected to the force from the wall molecules. The force can then be determined by the position of the molecule relative to the wall. This model avoids excessive calculations of fluid-wall interactions and reduces the computational time drastically. The time reduction is significant for small fluid density and channel height. The virtual-wall model is applied to Poiseuille and Couette flows, and to a flow in a channel with a rough surface. Results of the virtual and atomic wall simulations agree well with each other, thereby indicating the usefulness of the virtual-wall model. The appropriate bin size and cut-off radius in the virtual-wall model are also discussed. |
format | Online Article Text |
id | pubmed-6274448 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-62744482018-12-28 Virtual-Wall Model for Molecular Dynamics Simulation Qian, Lijuan Tu, Chengxu Bao, Fubing Zhang, Yonghao Molecules Article A large number of molecules are usually required to model atomic walls in molecular dynamics simulations. A virtual-wall model is proposed in this study to describe fluid-wall molecular interactions, for reducing the computational time. The infinite repetition of unit cell structures within the atomic wall causes the periodicity of the force acting on a fluid molecule from the wall molecules. This force is first calculated and then stored in the memory. A fluid molecule appearing in the wall force field is subjected to the force from the wall molecules. The force can then be determined by the position of the molecule relative to the wall. This model avoids excessive calculations of fluid-wall interactions and reduces the computational time drastically. The time reduction is significant for small fluid density and channel height. The virtual-wall model is applied to Poiseuille and Couette flows, and to a flow in a channel with a rough surface. Results of the virtual and atomic wall simulations agree well with each other, thereby indicating the usefulness of the virtual-wall model. The appropriate bin size and cut-off radius in the virtual-wall model are also discussed. MDPI 2016-12-09 /pmc/articles/PMC6274448/ /pubmed/27941688 http://dx.doi.org/10.3390/molecules21121678 Text en © 2016 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC-BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Qian, Lijuan Tu, Chengxu Bao, Fubing Zhang, Yonghao Virtual-Wall Model for Molecular Dynamics Simulation |
title | Virtual-Wall Model for Molecular Dynamics Simulation |
title_full | Virtual-Wall Model for Molecular Dynamics Simulation |
title_fullStr | Virtual-Wall Model for Molecular Dynamics Simulation |
title_full_unstemmed | Virtual-Wall Model for Molecular Dynamics Simulation |
title_short | Virtual-Wall Model for Molecular Dynamics Simulation |
title_sort | virtual-wall model for molecular dynamics simulation |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6274448/ https://www.ncbi.nlm.nih.gov/pubmed/27941688 http://dx.doi.org/10.3390/molecules21121678 |
work_keys_str_mv | AT qianlijuan virtualwallmodelformoleculardynamicssimulation AT tuchengxu virtualwallmodelformoleculardynamicssimulation AT baofubing virtualwallmodelformoleculardynamicssimulation AT zhangyonghao virtualwallmodelformoleculardynamicssimulation |