Petascale molecular dynamics simulation using the fast multipole method on K computer

Yousuke Ohno, Rio Yokota, Hiroshi Koyama, Gentaro Morimoto, Aki Hasegawa, Gen Masumoto, Noriaki Okimoto, Yoshinori Hirano, Huda Ibeid, Tetsu Narumi, Makoto Taiji

Research output: Contribution to journalArticlepeer-review

16 Scopus citations

Abstract

In this paper, we report all-atom simulations of molecular crowding - a result from the full node simulation on the "K computer", which is a 10-PFLOPS supercomputer in Japan. The capability of this machine enables us to perform simulation of crowded cellular environments, which are more realistic compared to conventional MD simulations where proteins are simulated in isolation. Living cells are "crowded" because macromolecules comprise ∼30% of their molecular weight. Recently, the effects of crowded cellular environments on protein stability have been revealed through in-cell NMR spectroscopy. To measure the performance of the "K computer", we performed all-atom classical molecular dynamics simulations of two systems: target proteins in a solvent, and target proteins in an environment of molecular crowders that mimic the conditions of a living cell. Using the full system, we achieved 4.4 PFLOPS during a 520 million-atom simulation with cutoff of 28 Å. Furthermore, we discuss the performance and scaling of fast multipole methods for molecular dynamics simulations on the "K computer", as well as comparisons with Ewald summation methods. © 2014 Elsevier B.V. All rights reserved.
Original languageEnglish (US)
Pages (from-to)2575-2585
Number of pages11
JournalComputer Physics Communications
Volume185
Issue number10
DOIs
StatePublished - Oct 2014

ASJC Scopus subject areas

  • Hardware and Architecture
  • Physics and Astronomy(all)

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