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Using special-purpose hardware to achieve a hundred-fold speedup in molecular dynamics simulations of proteins

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1 Author(s)
David Shaw ; D. E. Shaw Research and Center for Computational Biology and Bioinformatics, Columbia University, USA

Summary form only given. Molecular dynamics (MD) simulation has long been recognized as a potentially transformative tool for understanding the behavior of proteins and other biological macromolecules, and for developing a new generation of precisely targeted drugs. Many biologically important phenomena, however, occur over timescales that have previously fallen far outside the reach of MD technology. We have constructed a specialized, massively parallel machine, called Anton, that is capable of performing atomic-level simulations of proteins at a speed roughly two orders of magnitude beyond that of the previous state of the art. The machine has now simulated the behavior of a number of proteins for periods as long as a millisecond -- approximately 100 times the length of the longest such simulation previously published -- revealing aspects of protein dynamics that were previously inaccessible to both computational and experimental study. The speed at which Anton performs these simulations is the result of a tightly coupled codesign process in which novel algorithms and architectural features were developed in concert, guided in large part by an iterative process of performance analysis and optimization.

Published in:

Performance Analysis of Systems & Software (ISPASS), 2010 IEEE International Symposium on

Date of Conference:

28-30 March 2010