Are Gaming-Enabled Graphic Processing Unit Cards Convenient for Molecular Dynamics Simulation?

Tommaso Biagini, Francesco Petrizzelli, Mauro Truglio, Roberto Cespa, Alessandro Barbieri, Daniele Capocefalo, Stefano Castellana, Maria Florencia Tevy, Massimo Carella, Tommaso Mazza

Research output: Contribution to journalComment/debate

Abstract

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.

Original languageEnglish
JournalEvolutionary Bioinformatics
Volume15
DOIs
Publication statusPublished - May 1 2019

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Keywords

  • GPU computing
  • molecular dynamics simulation
  • protein structure

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Computer Science Applications

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