GPU Programming for Molecular Modeling Workshop Lecture Materials


CUDA/OpenCL Example Source Codes

Reading materials:

Publications Database GPU-accelerated molecular modeling coming of age. John E. Stone, David J. Hardy, Ivan S. Ufimtsev, and Klaus Schulten. Journal of Molecular Graphics and Modelling, 29:116-125, 2010.

Fast Molecular Electrostatics Algorithms on GPUs David J. Hardy, John E. Stone, Kirby L. Vandivort, David Gohara, Christopher Rodrigues, and Klaus Schulten. In, GPU Computing Gems, 2010. In press.

GPU-Accelerated Computation and Interactive Display of Molecular Orbitals John E. Stone, David J. Hardy, Jan Saam, Kirby L. Vandivort, and Klaus Schulten. In, GPU Computing Gems, 2010. In press.

Long time-scale simulations of in vivo diffusion using GPU hardware. Elijah Roberts, John E. Stone, Leonardo Sepulveda, Wen-mei W. Hwu, and Zaida Luthey-Schulten. In IPDPS '09: Proceedings of the 2009 IEEE International Symposium on Parallel & Distributed Processing, pp. 1-8, 2009

Publications Database Adapting a message-driven parallel application to GPU-accelerated clusters. James C. Phillips, John E. Stone, and Klaus Schulten. In SC '08: Proceedings of the 2008 ACM/IEEE Conference on Supercomputing, Piscataway, NJ, USA, 2008. IEEE Press. (9 pages). Publications Database Accelerating molecular modeling applications with graphics processors. John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco, and Klaus Schulten. Journal of Computational Chemistry, 28:2618-2640, 2007. GPU molecular modeling research home page