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ABSTRACT: Computational grids are a promising resource for modeling complex biochemical processes such as protein folding, penetration of gases or water into proteins, or protein structural rearrangements coupled to ligand binding. We have enabled the molecular dynamics program CHARMM to run on the Open Science Grid. The implementation is general, flexible, easily modifiable for use with other molecular dynamics programs and other grids and automated in terms of job submission, monitoring, and resubmission. The usefulness of grid computing was demonstrated through the study of hydration of the Glu-66 side chain in the interior of protein staphylococcal nuclease. Multiple simulations started with and without two internal water molecules shown crystallographically to be associated with the side chain of Glu-66 yielded two distinct populations of rotameric states of Glu-66 that differed by as much as 20%. This illustrates how internal water molecules can bias protein conformations. Furthermore, there appeared to be a temporal correlation between dehydration of the side chain and conformational transitions of Glu-66. This example demonstrated how difficult it is to get convergence even in the relatively simple case of a side chain oscillating between two conformations. With grid computing, we also benchmarked the self-guided Langevin dynamics method against the Langevin dynamics method traditionally used for temperature control in molecular dynamics simulations and showed that the two methods yield comparable results.
Journal of Chemical Information and Modeling 11/2008; 48(10):2021-9. · 4.07 Impact Factor