Studying protein folding on the Grid: Experiences using CHARMM on NPACI resources under legion

  • Natrajan A
  • Crowley M
  • Wilkins-Diehr N
 et al. 
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Abstract

One benefit of a computational Grid is the ability to run high-performance applications over distributed resources simply and securely. We demonstrated this benefit with an experiment in which we studied the protein-folding process with the CHARMM molecular simulation package over a Grid managed by Legion, a Grid operating system. High-performance applications can take advantage of Grid resources if the Grid operating system provides both low-level functionality as well as high-level services. We describe the nature of services provided by Legion for high-performance applications. Our experiences indicate that human factors continue to play a crucial role in the configuration of Grid resources, underlying resources can be problematic, Grid services must tolerate underlying problems or inform the user, and high-level services must continue to evolve to meet user requirements. Our experiment not only helped a scientist perform an important study, but also showed the viability of an integrated approach such as Legion's for managing a Grid. Copyright © 2004 John Wiley & Sons, Ltd.An earlier version of this paper has been published under the same title in the Proceedings of the 10th International Symposium on High Performance Distributed Computing (HPDC-10) [1]

Author-supplied keywords

  • CHARMM
  • Computational grid
  • Legion
  • Protein folding

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Authors

  • Anand Natrajan

  • Michael Crowley

  • Nancy Wilkins-Diehr

  • Marty A. Humphrey

  • Anthony D. Fox

  • Andrew S. Grimshaw

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