Grid computing and biomolecular simulation

Christopher J. Woods, Muan Hong Ng, Steven Johnston, Stuart E. Murdock, Bing Wu, Kaihsu Tai, Hans Fangohr, Paul Jeffreys, Simon Cox, Jeremy G. Frey, Mark S. P. Sansom, Jonathan W. Essex

Research output: Contribution to journalArticlepeer-review


Biomolecular computer simulations are now widely used not only in an academic setting to understand the fundamental role of molecular dynamics on biological function, but also in the industrial context to assist in drug design.In this paper, two applications of Grid computing to this area will be outlined. The first, involving the coupling of distributed computing resources to dedicated Beowulf clusters, is targeted at simulating protein conformational change using the Replica Exchange methodology. In the second, the rationale and design of a database of biomolecular simulation trajectories is described. Both applications illustrate the increasingly important role modern computational methods are playing in the life sciences.
Original languageEnglish
Pages (from-to)2017-2035
Number of pages19
JournalPhilosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences
Issue number1833
Early online date26 Jul 2005
Publication statusPublished - 15 Aug 2005


  • grid
  • replica exchange
  • protein conformation
  • simulation trajectory
  • storage
  • analysis free-energy calculations
  • molecular-dynamics
  • integration


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