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GPU-Optimized Coarse-Grained MD Simulations of Protein and RNA Folding and Assembly

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Executive Summary

Molecular Dynamics (MD) simulations provide a molecular-resolution physical description of the folding and assembly processes, but the size and the timescales of simulations are limited because the underlying algorithm is computationally demanding. The authors recently introduced a parallel neighbor list algorithm that was specifically optimized for MD simulations on GPUs. In their present paper, they analyze the performance of the algorithm in their MD simulation software, and they observe that the major of the overall execution time is spent performing the force calculations and the evaluation of the neighbor list and pair lists.

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