Wednesday, March 12

MS10
Current Developments in High-Performance Molecular Dynamics Simulations - Part II of II

3:15 PM - 5:15 PM
Room: Atlanta A

For Part I, see MS2

Molecular dynamics (MD) simulations, which model the motion of atoms within a molecular system, can serve as a computational “microscope” onto phenomena that are difficult to observe experimentally. Thanks to improvements in both algorithms and computational hardware, accurate MD simulations will soon be able to access the microsecond and millisecond time scales characteristic of some of the biochemical events of greatest scientific and pharmaceutical interest. The huge computational requirements of such simulations demand parallel computation, as well as new algorithms and implementations that efficiently parallelize the various components of the interatomic force calculation. In this minisymposium, we examine the latest progress in several high-performance approaches to MD simulation. These approaches include parallel supercomputers using processors specifically designed for MD, new implementations using commodity graphics processors, and novel algorithms for general-purpose supercomputers and clusters.

Organizer: David E. Shaw
D. E. Shaw Research and Columbia University
Edmond Chow
D. E. Shaw Research
Ron O. Dror
D. E. Shaw Research

3:15-3:40 Scaling Classical Molecular Dynamics to O(1) Atom per Node

Robert S. Germain, Blake G. Fitch, Aleksandr Rayshubskiy, Maria Eleftheriou, Christopher Ward, and Michael C. Pitman, IBM T.J. Watson Research Center

3:45-4:10 Petascale Special-Purpose Computer for Molecular Dynamics Simulations: MDGRAPE-3 and Beyond

Makoto Taiji, Tetsu Narumi, and Yosuke Ohno, RIKEN Genomic Sciences Center, Japan; Duraid Madeina and Takashi Ikegami, University of Tokyo, Japan

4:15-4:40 Accelerating NAMD with Graphics Processors

James C. Phillips, John E. Stone, and Klaus Schulten, University of Illinois at Urbana-Champaign

4:45-5:10 Anton: A Special-purpose Machine for Molecular Dynamics Simulation

David E. Shaw, D. E. Shaw Research and Columbia University ; Martin M. Deneroff, Ron O. Dror, Jeffrey S. Kuskin, Richard H. Larson, John K. Salmon, and Cliff Young, D. E. Shaw Research