Cargando…
Are Gaming-Enabled Graphic Processing Unit Cards Convenient for Molecular Dynamics Simulation?
In several fields of research, molecular dynamics simulation techniques are exploited to evaluate the temporal motion of particles constituting water, ions, small molecules, macromolecules, or more complex systems over time. These techniques are considered difficult to setup, computationally demandi...
Autores principales: | , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
SAGE Publications
2019
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6537481/ https://www.ncbi.nlm.nih.gov/pubmed/31205410 http://dx.doi.org/10.1177/1176934319850144 |
_version_ | 1783422021038768128 |
---|---|
author | Biagini, Tommaso Petrizzelli, Francesco Truglio, Mauro Cespa, Roberto Barbieri, Alessandro Capocefalo, Daniele Castellana, Stefano Tevy, Maria Florencia Carella, Massimo Mazza, Tommaso |
author_facet | Biagini, Tommaso Petrizzelli, Francesco Truglio, Mauro Cespa, Roberto Barbieri, Alessandro Capocefalo, Daniele Castellana, Stefano Tevy, Maria Florencia Carella, Massimo Mazza, Tommaso |
author_sort | Biagini, Tommaso |
collection | PubMed |
description | In several fields of research, molecular dynamics simulation techniques are exploited to evaluate the temporal motion of particles constituting water, ions, small molecules, macromolecules, or more complex systems over time. These techniques are considered difficult to setup, computationally demanding and require high specialization and scientific skills. Moreover, they need specialized computing infrastructures to run faster and make the simulation of big systems feasible. Here, we have simulated 3 systems of increasing sizes on scientific- and gaming-enabled graphic processing unit (GPU) cards with Amber, GROMACS, and NAMD and measured their performance accounting also for the market prices of the GPU cards where they were run on. |
format | Online Article Text |
id | pubmed-6537481 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | SAGE Publications |
record_format | MEDLINE/PubMed |
spelling | pubmed-65374812019-06-14 Are Gaming-Enabled Graphic Processing Unit Cards Convenient for Molecular Dynamics Simulation? Biagini, Tommaso Petrizzelli, Francesco Truglio, Mauro Cespa, Roberto Barbieri, Alessandro Capocefalo, Daniele Castellana, Stefano Tevy, Maria Florencia Carella, Massimo Mazza, Tommaso Evol Bioinform Online Commentary In several fields of research, molecular dynamics simulation techniques are exploited to evaluate the temporal motion of particles constituting water, ions, small molecules, macromolecules, or more complex systems over time. These techniques are considered difficult to setup, computationally demanding and require high specialization and scientific skills. Moreover, they need specialized computing infrastructures to run faster and make the simulation of big systems feasible. Here, we have simulated 3 systems of increasing sizes on scientific- and gaming-enabled graphic processing unit (GPU) cards with Amber, GROMACS, and NAMD and measured their performance accounting also for the market prices of the GPU cards where they were run on. SAGE Publications 2019-05-22 /pmc/articles/PMC6537481/ /pubmed/31205410 http://dx.doi.org/10.1177/1176934319850144 Text en © The Author(s) 2019 http://creativecommons.org/licenses/by-nc/4.0/ This article is distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 License (http://www.creativecommons.org/licenses/by-nc/4.0/) which permits non-commercial use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access pages (https://us.sagepub.com/en-us/nam/open-access-at-sage). |
spellingShingle | Commentary Biagini, Tommaso Petrizzelli, Francesco Truglio, Mauro Cespa, Roberto Barbieri, Alessandro Capocefalo, Daniele Castellana, Stefano Tevy, Maria Florencia Carella, Massimo Mazza, Tommaso Are Gaming-Enabled Graphic Processing Unit Cards Convenient for Molecular Dynamics Simulation? |
title | Are Gaming-Enabled Graphic Processing Unit Cards Convenient for Molecular Dynamics Simulation? |
title_full | Are Gaming-Enabled Graphic Processing Unit Cards Convenient for Molecular Dynamics Simulation? |
title_fullStr | Are Gaming-Enabled Graphic Processing Unit Cards Convenient for Molecular Dynamics Simulation? |
title_full_unstemmed | Are Gaming-Enabled Graphic Processing Unit Cards Convenient for Molecular Dynamics Simulation? |
title_short | Are Gaming-Enabled Graphic Processing Unit Cards Convenient for Molecular Dynamics Simulation? |
title_sort | are gaming-enabled graphic processing unit cards convenient for molecular dynamics simulation? |
topic | Commentary |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6537481/ https://www.ncbi.nlm.nih.gov/pubmed/31205410 http://dx.doi.org/10.1177/1176934319850144 |
work_keys_str_mv | AT biaginitommaso aregamingenabledgraphicprocessingunitcardsconvenientformoleculardynamicssimulation AT petrizzellifrancesco aregamingenabledgraphicprocessingunitcardsconvenientformoleculardynamicssimulation AT trugliomauro aregamingenabledgraphicprocessingunitcardsconvenientformoleculardynamicssimulation AT cesparoberto aregamingenabledgraphicprocessingunitcardsconvenientformoleculardynamicssimulation AT barbierialessandro aregamingenabledgraphicprocessingunitcardsconvenientformoleculardynamicssimulation AT capocefalodaniele aregamingenabledgraphicprocessingunitcardsconvenientformoleculardynamicssimulation AT castellanastefano aregamingenabledgraphicprocessingunitcardsconvenientformoleculardynamicssimulation AT tevymariaflorencia aregamingenabledgraphicprocessingunitcardsconvenientformoleculardynamicssimulation AT carellamassimo aregamingenabledgraphicprocessingunitcardsconvenientformoleculardynamicssimulation AT mazzatommaso aregamingenabledgraphicprocessingunitcardsconvenientformoleculardynamicssimulation |