Paper Citing NAMD - Abstract
Shaw, David E.; Dror, Ron O.; Salmon, John K.; Grossman, J. P.; Mackenzie, Kenneth M.; Bank, Joseph A.; Young, Cliff; Deneroff, Martin M.; Batson, Brannon; Bowers, Kevin J.; Chow, Edmond; Eastwood, Michael P.; Ierardi, Douglas J.; Klepeis, John L.; Kuskin, Jeffrey S.; Larson, Richard H.; Lindorff-Larsen, Kresten; Maragakis, Paul; Moraes, Mark A.; Piana, Stefano; Shan, Yibing; Towles, Brian
Millisecond-Scale Molecular Dynamics Simulations on Anton
PROCEEDINGS OF THE CONFERENCE ON HIGH PERFORMANCE COMPUTING NETWORKING, STORAGE AND ANALYSIS, , 2009
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.
