TCB Publications - Abstract

Michelle Gower, Jordi Cohen, James Phillips, Richard Kufrin, and Klaus Schulten. Managing biomolecular simulations in a grid environment with NAMD-G. In Proceedings of the 2006 TeraGrid Conference, 2006. (7 pages).

GOWE2006 Experiences designing and deploying NAMD-G, an infrastructure for executing biomolecular simulations using the parallel molecular dynamics code NAMD within the context of a Computational Grid, are described. The effort is motivated by a general outline of the tasks involved in conducting research of this class as traditionally undertaken, followed by a description of the enhancements offered by current developments in Grid technologies. Specifics of the initial implementation of NAMD-G are given and a brief example of the use of the system in real-world scientific investigations simulating gas permeation in proteins is provided.

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