Title: Biomolecular Modeling with VMD and NAMD accelerated through graphics processing units

Abstract:
In this lecture I will summarize recent attempts to employ graphics processing units (GPU) to accelerate key computational tasks that arise in biomolecular modeling. The acceleration has been achieved using NVIDIA GPUs and CUDA. Tasks that were accelerated are standardmoelcular dynamics, evaluation of electrostatic potentials for 100 miliion atom structures, and rendering of complex quantum chemistry data as they arise in QM/MM calculations.

John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco, and Klaus Schulten. Accelerating molecular modeling applications with graphics processors. Journal of Computational Chemistry, 28:2618-2640, 2007.

Christopher I. Rodrigues, David J. Hardy, John E. Stone, Klaus Schulten, and Wen-Mei W. Hwu. GPU acceleration of cutoff pair potentials for molecular modeling applications. In CF'08: Proceedings of the 2008 conference on Computing frontiers, pp. 273-282, New York, NY, USA, 2008. ACM.

David J. Hardy, John E. Stone, and Klaus Schulten. Multilevel summation of electrostatic potentials using graphics processing units. Journal of Parallel Computing, 2009. In press.

James C. Phillips, John E. Stone, and Klaus Schulten. Adapting a message-driven parallel application to GPU-accelerated clusters. In SC '08: Proceedings of the 2008 ACM/IEEE Conference on Supercomputing, pp. 1-9, Piscataway, NJ, USA, 2008. IEEE Press.

John E. Stone, Jan Saam, David J. Hardy, Kirby L. Vandivort, Wen mei W. Hwu, and Klaus Schulten. High performance computation and interactive display of molecular orbitals on GPUs and multi-core CPUs. In Second Workshop on General-Purpose Computation on Graphics Processing Units, 2009. In press.