A comparison between parallelization approaches in molecular dynamics   simulations on GPUs
  We test the performances of two different approaches to the computation of forces for molecular dynamics simulations on Graphics Processing Units. A "vertex-based" approach, where a computing thread is started per particle, is compared to a newly proposed "edge-based" approach, where a thread is started per each potentially non-zero interaction. We find that the former is more efficient for systems with many simple interactions per particle, while the latter is more efficient if the system has more complicated interactions or fewer of them. By comparing computation times on more and less recent GPU technology, we predict that, if the current trend of increasing the number of processing cores - as opposed to their computing power - remains, the "edge-based" approach will gradually become the most efficient choice in an increasing number of cases. 
Lorenzo Rovigatti, Petr \v{S}ulc, Istv\'an Z. Reguly, Flavio Romano
physics.comp-ph cond-mat.soft