Managing Biomolecular Simulations in a Grid Environment with NAMD-G

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.