Studying protein folding on the grid: experiences using CHARMM on NPACI resources under Legion

Abstract

One benefit of a computational grid is the ability to run high-performance applications over distributed resources simply and securely. We demonstrate 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.