GPU-SD and DPD Parallelization for Gromacs tools for molecular dynamics simulations

Nicolae Goga, Siewert Marrink, Ruxandra Cioromela, Florica Moldoveanu

Research output: Chapter in Book/Report/Conference proceedingConference contributionAcademic

6 Citations (Scopus)
236 Downloads (Pure)

Abstract

This article presents the GPU parallelization of new algorithms SD and DPD types for molecular dynamics systems developed by the Molecular Dynamics Group, University of Groningen, the Netherlands. One should note that molecular dynamics simulations are time-consuming simulations of systems, running time ranging from days to weeks and months. Therefore parallelization is a key issue for the well-running and use of MD software. The paper presents the main ingredients of GPU parallelization of the new algorithms and simulation results. It can be concluded that the parallelization through the use of graphical cards improves the performances of the runs as compared to the serial version of the code.
Original languageEnglish
Title of host publicationProceedings of the 2012 IEEE 12th International Conference on Bioinformatics
PublisherIEEE (The Institute of Electrical and Electronics Engineers)
Pages251-254
Number of pages4
ISBN (Electronic)9781467343589
ISBN (Print)9781467343572
Publication statusPublished - 2012
Event2012 IEEE 12th International Conference on Bioinformatics -
Duration: 11-Nov-201213-Nov-2012

Conference

Conference2012 IEEE 12th International Conference on Bioinformatics
Period11/11/201213/11/2012

Keywords

  • CUDA programing
  • graphic cards systems
  • molecular dynamic systems

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