AMBER4 Port to T3D

Ken Merz

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Scientific Significance:

Amber4 is a suite of programs designed for molecular modeling and simulations. It is a robust package prominent in the toolkits of computational chemistry and biology researchers, and its methods, tailored to the study of macromolecules in solution, have found widespread applicability in modeling complex biochemical processes and in the pharmaceuticals industry. Amber's genesis was in the application of classical mechanics (i.e. integration of Newton's equations of motion) to large molecular assemblies using fitted potentials to determine low-energy conformations, model biological processes, obtain bulk properties, etc. New versions of Amber have since introduced capabilities to treat nuclear magnetic resonance data, support free energy perturbation calculations, and otherwise implement the functionality required by its research audience.

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Numerical Approach and Performance:

A port of AMBER to the T3D has been accomplished. We are now adding dynamic load balancing, which is mostly complete, but requires additional debugging. We expect this to be done by year's end. We will then turn our attention to incorporating more portions of serial code in parallel form.

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