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ACM/IEEE SC 2006 Conference (SC'06)
Although molecular dynamics (MD) simulations of biomolecular systems often run for days to months, many events of great scientific interest and pharmaceutical relevance occur on long time scales that remain beyond reach. We present several new algorithms and implementation techniques that significantly accelerate parallel MD simulations compared with current stateof-the-art codes. These include a novel parallel decomposition method and message-passing techniques that reduce communicationdoi:10.1109/sc.2006.54 fatcat:yx2ivaz25zfppabjumlm7wvp7m