Paper Citing NAMD - Abstract
Shi, Guochun; Kindratenko, Volodymyr
Implementation of NAMD molecular dynamics non-bonded force-field on the Cell Broadband Engine processor
2008 IEEE INTERNATIONAL SYMPOSIUM ON PARALLEL & DISTRIBUTED PROCESSING, VOLS 1-8, 2985-2992, 2008
We present results of porting an important kernel of a production molecular dynamics simulation program, NAMD, to the Cell/B.E. processor. The non-bonded force-field kernel, as implemented in the NAMD SPEC 2006 CPU benchmark, has been implemented. Both single-precision and double-precision floating-point kernel variations are considered, and performance results obtained on the Cell/B.E., as well as several other platforms, are reported Our results obtained on a 3.2 GHz Cell/B.E. blade show linear speedups when using multiple synergistic processing elements.
