Solving Molecular Distance Geometry Problems in OpenCL

Istvan Lorentz, Razvan Andonie, Levente Fabry-Asztalos
Electronics and Computers Department, Transilvania University, Brasov, Romania
13th International Conference on Optimization of Electrical and Electronic Equipment (OPTIM’2012), 2012


   title={Solving Molecular Distance Geometry Problems in OpenCL},

   author={Lorentz, I. and Andonie, R. and Fabry-Asztalos, L.},



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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.
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