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In December 1999, IBM announced the start of a five-year effort to build a massively parallel computer, to be applied to the study of biomolecular phenomena such as protein folding. The project has two main goals: to advance our understanding of the mechanisms behind protein folding via large-scale simulation, and to explore novel ideas in massively… (More)

To meet the challenge of modeling the conformational dynamics of biological macromolecules over long time scales, much recent effort has been devoted to constructing stochastic kinetic models, often in the form of discrete-state Markov models, from short molecular dynamics simulations. To construct useful models that faithfully represent dynamics at the… (More)

This paper presents strong scaling performance data for the Blue Matter molecular dynamics framework using a novel n-body spatial decomposition and a collective communications technique implemented on both MPI and low level hardware interfaces. Using Blue Matter on Blue Gene/L, we have measured scalability through 16,384 nodes with measured time per… (More)

Protein folding involves physical timescales—microseconds to seconds—that are too long to be studied directly by straightforward molecular dynamics simulation, where the fundamental timestep is constrained to femtoseconds. Here we show how the long-time statistical dynamics of a simple solvated biomolecular system can be well described by a discrete-state… (More)

A rigorous formalism for the extraction of state-to-state transition functions from a Boltzmann-weighted ensemble of microcanonical molecular dynamics simulations has been developed as a way to study the kinetics of protein folding in the context of a Markov chain. Analysis of these transition functions for signatures of Markovian behavior is described. The… (More)

Hydration free energy calculations have become important tests of force fields. Alchemical free energy calculations based on molecular dynamics simulations provide a rigorous way to calculate these free energies for a particular force field, given sufficient sampling. Here, we report results of alchemical hydration free energy calculations for the set of… (More)

While developing the protein folding application for the IBM Blue Genet/L supercomputer, some frequently executed computational kernels were encountered. These were significantly more complex than the linear algebra kernels that are normally provided as tuned libraries with modern machines. Using regular library functions for these would have resulted in an… (More)