Accelerating Molecular Structure Determination Based on Inter-Atomic Distances Using OpenCL

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Computer Science

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Fast and accurate determination of the 3D structure of molecules is essential for better understanding their physical, chemical, and biological properties. We focus on an existing method for molecular structure determination: restrained molecular dynamics with simulated annealing. In this method a hybrid function, composed by a physical model and experimental restraints, is minimized by simulated annealing. Our goal is to accelerate computation time using commodity multi-core CPUs and GPUs in a heterogeneous computing model. We present a parallel and portable OpenCL implementation of this method. Experimental results are discussed in terms of accuracy, execution time, and parallel scalability. With respect to the XPLOR-NIH professional software package, compared to the single CPU core implementation, we obtain speedups of three to five times (increasing with problem size) on commodity GPUs. We achieve these performances by writing specialized kernels for different problem sizes and hardware architectures.


This article was originally published in IEEE Transactions on Parallel and Distributed Systems. The full-text article from the publisher can be found here.

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IEEE Transactions on Parallel and Distributed Systems


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