Molecular dynamics (MD) simulations are widely used to study protein motions at an atomic level of detail, but they have been limited to time scales shorter than those of many biologically critical conformational changes. We examined two fundamental processes in protein dynamics--protein folding and conformational change within the folded state--by means of extremely long all-atom MD simulations conducted on a special-purpose machine. Equilibrium simulations of a WW protein domain captured multiple folding and unfolding events that consistently follow a well-defined folding pathway; separate simulations of the protein's constituent substructures shed light on possible determinants of this pathway. A 1-millisecond simulation of the folded protein BPTI reveals a small number of structurally distinct conformational states whose reversible interconversion is slower than local relaxations within those states by a factor of more than 1000.

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Anton, a massively parallel special-purpose machine for molecular dynamics simulations, performs a 32×32×32 FFT in 3.7 microseconds and a 64×64×64 FFT in 13.3 microseconds on a configuration with 512 nodes-an order of magnitude faster than all other FFT implementations of which we are aware. Achieving this FFT performance requires a coordinated combination of computation and communication techniques that leverage Anton's underlying hardware mechanisms. Most significantly, Anton's communication subsystem provides over 300 gigabits per second of bandwidth per node, message latency in the hundreds of nanoseconds, and support for word-level writes and single-ended communication. In addition, Anton's general-purpose computation system incorporates primitives that support the efficient parallelization of small 1D FFTs. Although Anton was designed specifically for molecular dynamics simulations, a number of the hardware primitives and software implementation techniques described in this paper may also be applicable to the acceleration of FFTs on general-purpose high-performance machines.