Computer simulation using particles
Computer simulation using particles
Symplectic integration with floating-point arithmetic and other approximations
proceedings of the on Numerical analysis of hamiltonian differential equations
NAMD2: greater scalability for parallel molecular dynamics
Journal of Computational Physics - Special issue on computational molecular biophysics
Supercomputing '96 Proceedings of the 1996 ACM/IEEE conference on Supercomputing
Blue matter on blue gene/L: massively parallel computation for biomolecular simulation
CODES+ISSS '05 Proceedings of the 3rd IEEE/ACM/IFIP international conference on Hardware/software codesign and system synthesis
Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Scalable algorithms for molecular dynamics simulations on commodity clusters
Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Blue matter: approaching the limits of concurrency for classical molecular dynamics
Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Zonal methods for the parallel execution of range-limited N-body simulations
Journal of Computational Physics
Anton, a special-purpose machine for molecular dynamics simulation
Proceedings of the 34th annual international symposium on Computer architecture
A 32x32x32, spatially distributed 3D FFT in four microseconds on Anton
Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis
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Anton is a recently completed special-purpose supercomputer designed for molecular dynamics (MD) simulations of biomolecular systems. The machine's specialized hardware dramatically increases the speed of MD calculations, making possible for the first time the simulation of biological molecules at an atomic level of detail for periods on the order of a millisecond---about two orders of magnitude beyond the previous state of the art. Anton is now running simulations on a timescale at which many critically important, but poorly understood phenomena are known to occur, allowing the observation of aspects of protein dynamics that were previously inaccessible to both computational and experimental study. Here, we report Anton's performance when executing actual MD simulations whose accuracy has been validated against both existing MD software and experimental observations. We also discuss the manner in which novel algorithms have been coordinated with Anton's co-designed, application-specific hardware to achieve these results.