Molecular Simulations On Supercomputers

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Abstract
Work from our laboratory using molecular dynamics applied to the study of peptide/protein folding dynam ics and thermodynamics in aqueous solution, and the exploration and development of molecular solvent in teraction models including electronic polarizability is described. The basic computational techniques we have used in developing algorithms for vector/parallel, shared memory, multiple instruction, multiple data (MIMD) and massively parallel single instruction, multi ple data (SIMD) architectures are discussed in the con text of these application areas. The technique we have used to parallelize the molecular dynamics/molecular mechanics code CHARMM is detailed, with special fo cus given to the performance issues faced in develop ing algorithms for the CRAY Y-MP. New developments of a molecular dynamics kernel for simulation of elec tronically polarizable solvent systems using a parallel- extended Fortran language (Fortran-9X) on the mas sively parallel Connection Machine (CM-2) are out lined. We provide examples of applications using both of these platforms and discuss the development of software for such simulations in a heterogeneous com putational environment.