Parallel Algorithms and Architectures for Millisecond-Scale Molecular Dynamics Simulations of Proteins

The ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macromolecules could in principle lead to important scientific advances and provide a powerful new tool for drug discovery. A wide range of biologically interesting phenomena, however, occur over time scales on the order of a millisecond—about three orders of magnitude beyond the duration of the longest current MD simulations. This talk will describe our research on massively parallel machine architectures and algorithms for the execution of millisecond-scale MD simulations of biological macromolecules. Special emphasis will be given to a new class of methods for parallelizing the range-limited n-body problem that offer both asymptotic and absolute advantages by comparison with traditional spatial decomposition methods.

David E. Shaw, D. E. Shaw Research and Columbia University



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