Solving molecular distance geometry problems in OpenCL

Istvan Lorentz, Razvan Andonie, Levente Fabry-Asztalos
2012 2012 13th International Conference on Optimization of Electrical and Electronic Equipment (OPTIM)  
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 breadthfirst search and geometric buildup) and its OpenCL parallel implementation. The approach has the potential to speed up computation of
more » ... -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.
doi:10.1109/optim.2012.6231916 fatcat:qs6youvao5djfoaiwckkb27nqm