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Studying protein folding on the Grid: experiences using CHARMM on NPACI resources under Legion
Author(s) -
Natrajan Anand,
Crowley Michael,
WilkinsDiehr Nancy,
Humphrey Marty A.,
Fox Anthony D.,
Grimshaw Andrew S.,
Brooks Charles L.
Publication year - 2004
Publication title -
concurrency and computation: practice and experience
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.309
H-Index - 67
eISSN - 1532-0634
pISSN - 1532-0626
DOI - 10.1002/cpe.763
Subject(s) - grid , computer science , grid computing , distributed computing , folding (dsp implementation) , process (computing) , semantic grid , drmaa , world wide web , operating system , engineering , electrical engineering , semantic web , geometry , mathematics
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.