Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation. In Proceedings of the 2014 International Conference for High Performance Computing, Networking, Storage, and Analysis (SC14), 2014. Wozniak, Michael Wilde, and Klaus Schulten. Petascale Tcl with NAMD, VMD, and Swift/T. In SC'14 workshop on High Performance Technical Computing in Dynamic Languages, SC '14. Wei Jiang, James Phillips, Lei Huang, Mikolai Fajer, Yilin Meng, James Gumbart, Yun Luo, Klaus Schulten, and Benoit Roux. Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD.Ĭomputer Physics Communications, 185:908-916, 2014. ![]() Yanhua Sun, Gengbin Zheng, Chao Mei, Eric J. Optimizing Fine-grained Communication in a Biomolecular Simulation Application on Cray XK6. In Proceedings of the 2012 ACM/IEEE Conference on Supercomputing (SC12), 2012.ĭavid E. ![]() GPU/CPU algorithm for generalized Born / solvent-accessible surface area implicit solvent calculations. Journal of Chemical Theory and Computation, 8:2521-2530, 2012.ĭavid E.
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