NAMD: Scalable molecular dynamics based on the charm++ parallel runtime system

Bilge Acun, Ronak Buch, Laxmikant V Kale, James C. Phillips

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Nanoscale Molecular Dynamics (NAMD) is a scalable molecular dynamics (MD) application designed for high-performance atomic-level simulation of large biomolecular systems at a femtosecond time step resolution [1]. Used by tens of thousands of scientists-85,000 users since 2000-on everything from laptops and desktops to supercomputers and graphical processing units (GPUs) (even iPads!), NAMD has enabled significant breakthroughs in understanding the structure and the behavior of viruses and cellular organelles.

Original languageEnglish (US)
Title of host publicationExascale Scientific Applications
Subtitle of host publicationScalability and Performance Portability
EditorsTjerk P Straatsma, Katerina B Antypas, Timothy J Williams
PublisherCRC Press
Pages119-143
Number of pages25
ISBN (Electronic)9781351999243
ISBN (Print)9781138197541
DOIs
StatePublished - Jan 1 2017

ASJC Scopus subject areas

  • Computer Science(all)
  • Mathematics(all)
  • Physics and Astronomy(all)

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  • Cite this

    Acun, B., Buch, R., Kale, L. V., & Phillips, J. C. (2017). NAMD: Scalable molecular dynamics based on the charm++ parallel runtime system. In T. P. Straatsma, K. B. Antypas, & T. J. Williams (Eds.), Exascale Scientific Applications: Scalability and Performance Portability (pp. 119-143). CRC Press. https://doi.org/10.1201/b21930-5