Solving molecular distance geometry problems in OpenCL
Document Type
Conference Proceeding
Department or Administrative Unit
Computer Science
Publication Date
5-24-2012
Abstract
We focus on the following computational chemistry problem: Given a subset of the exact distances between atoms, reconstruct the three-dimensional position of each atom in the given molecule. The distance matrix is generally sparse. This problem is both important and challenging. Our contribution is a novel combination of two known techniques (parallel breadth-first search and geometric buildup) and its OpenCL parallel implementation. The approach has the potential to speed up computation of three-dimensional structures of molecules - a critical process in computational chemistry. From experiments on multi-core CPUs and graphic processing units, we conclude that, for sufficient large problems, our implementation shows a moderate scalability.
Recommended Citation
Lorentz, I., Andonie, R., & Fabry-Asztalos, L. (2012). Solving molecular distance geometry problems in OpenCL. 2012 13th International Conference on Optimization of Electrical and Electronic Equipment (OPTIM). https://doi.org/10.1109/optim.2012.6231916
Journal
2012 13th International Conference on Optimization of Electrical and Electronic Equipment (OPTIM)
Rights
Copyright © 2012, IEEE
Comments
This article was originally published in 2012 13th International Conference on Optimization of Electrical and Electronic Equipment (OPTIM). The full-text article from the publisher can be found here.
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