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Langevin dynamics simulations of biomolecules on graphics processors

A. Zhmurov, R. I. Dima, Y. Kholodov, V. Barsegov
Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow region, Russia, 141700
arXiv:1003.1148 [cond-mat.soft] (4 Mar 2010)

@article{zhmurov2010langevin,

   title={Langevin dynamics simulations of biomolecules on graphics processors},

   author={Zhmurov, A. and Dima, RI and Kholodov, Y. and Barsegov, V.},

   journal={Arxiv preprint arXiv:1003.1148},

   year={2010}

}

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Due to the very long timescales involved (us-s), theoretical modeling of fundamental biological processes including folding, misfolding, and mechanical unraveling of biomolecules, under physiologically relevant conditions, is challenging even for distributed computing systems. Graphics Processing Units (GPUs) are emerging as an alternative programming platform to the more traditional CPUs as they provide high raw computational power that can be utilized in a wide range of scientific applications. Using a coarse-grained Self Organized Polymer (SOP) model, we have developed and tested the GPU-based implementation of Langevin simulations for proteins (SOP-GPU program). Simultaneous calculation of forces for all particles is implemented using either the particle based or the interacting pair based parallelization, which leads to a ~30-fold acceleration compared to an optimized CPU version of the program. We assess the computational performance of an end-to-end application of the SOP-GPU program, where all steps of the algorithm are running on the GPU, by profiling the associated simulation time and memory usage for a number of small proteins, long protein fibers, and large-size protein assemblies. The SOP-GPU package can now be used in the theoretical exploration of the mechanical properties of large-size protein systems to generate the force-extension and force-indentation profiles under the experimental conditions of force application, and to relate the results of single-molecule experiments in vitro and in silico.
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