Electrostatic force computation for bio-molecules on supercomputers with torus networks

Peter Rissland, Yuefan Deng

Research output: Contribution to journalArticlepeer-review


We present an application of the Ewald algorithm for electrostatic force computation on a supercomputer with a torus network, like those on QCDOC and BlueGene/L. Typical bio-molecular systems have thousands, possibly millions of atoms interacting, with simulation time ranging from microseconds to milliseconds. The most dominant time consuming calculation for bio-molecules is the electrostatic interactions. The importance of an efficient all-gather method is discussed, in particular for QCDOC since it does not have a network specific for global communication like the tree network on BlueGene/L. In addition, we demonstrate the ability for QCDOC to run non QCD (Quantum Chromodynamics) applications, in particular, electrostatic force computation on bio-molecules.

Original languageEnglish (US)
Pages (from-to)116-123
Number of pages8
JournalParallel Computing
Issue number2
StatePublished - Mar 2007


  • Ewald summation
  • Molecular dynamics

ASJC Scopus subject areas

  • Software
  • Theoretical Computer Science
  • Hardware and Architecture
  • Computer Networks and Communications
  • Computer Graphics and Computer-Aided Design
  • Artificial Intelligence


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