Abstract
NAMD is a parallel molecular dynamics software designed for high-performance simulations of large biomolecular systems. It scales from single computer up to hundreds of processors as high-end parallel platforms. Additionally, considering the evolution of Graphics Processing Units (GPUs) as a general purpose massively parallel co-processors, NAMD has included this kind of devices to leverage its computational power. In this work we analyze current NAMD GPU solution and develop an alternative based on Newton’s third law. The results shows a significant reduction of the execution time of GPU computations, of up to 20 % when compared with a highly tuned version of the original GPU-enabled NAMD.
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González, Y., Ezzatti, P., Paulino, M. (2016). Unleashing the Graphic Processing Units-Based Version of NAMD. In: Ortuño, F., Rojas, I. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2016. Lecture Notes in Computer Science(), vol 9656. Springer, Cham. https://doi.org/10.1007/978-3-319-31744-1_56
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DOI: https://doi.org/10.1007/978-3-319-31744-1_56
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