Molecular Dynamics Calculations of Proteins on a "Hypercube"Machine

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The development of molecular dynamics techniques and their application to proteins has created demands for computing time that are demonstrably not being met by presently available resources. Highly parallel computers offer an opportunity to satisfy this need economically, but so far this potential has not been realized. This work will develop software modifications for doing molecular dynamics of peptides and proteins, optionally in solution, and specifically with options for computing free energy differences. This development shall take place on a 24-node parallel computer, the newly announced "Chemputer", a parallel machine with hypercube architecture. The machine will be delivered with efficient software for molecular dynamics. The plan is to adapt this software to perform the most "modern" calculations. These extensions will be made generally available.