Development and evaluation of a GPU-optimized N-body term for the simulation of biomolecules

Timo Strunk, Moritz Wolf, Wolfgang Wenzel
Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
SimLab@KIT Workshop, 2010


   title={Development and evaluation of a GPU-optimized N-body term for the simulation of biomolecules},

   author={Strunk, T. and Wolf, M. and Wenzel, W.},

   booktitle={Computational Methods in Science and Engineering $ dProceedings of the Workshop SimLabs@ KIT, November 29-30, 2010, Karlsruhe, Germany},


   organization={KIT Scientific Publishing}


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Advancements in massively parallel sampling of the conformational space of biomolecules enables, for example, protein structure prediction, in-silico drug development and cell signaling. Despite the existence of highly distributed protein simulation architectures like POEM@HOME, there was no abundant computational resource both strong and serial strength and in parallel sampling. In this study we investigate the optimization of our N-body Lennard-Jones force field for the efficient Monte-Carlo sampling of small to medium-size biomolecules on massively parallel architectures, like modern GPUs. We benchmark both NVIDIA and AMD GPU chipsets in the OpenCL framework on comparison to CPU architectures. The N-body interactions are broken down into small local grids, which fit into the local GPU caches to permit simultaneous evaluation. Using the N-body term we accelerate the Lennard-Jones and Clash-Potential of the complete free-energy PFF02 [1] shown to fold a multitude of different protein-folds and implement a modified structure-based Lennard Jones force field. We proof the applicability of our novel force field by reversible folding-simulations of a three-helix protein using this Go-potential from completely unifolded structures.
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