title: A comparison of neighbor search algorithms for large rigid molecules.
abstract: Fast determination of neighboring atoms is an essential step in molecular dynamics simulations or Monte Carlo computations, and there exists a variety of algorithms to efficiently compute neighbor lists. However, most of these algorithms are general, and not specifically designed for a given type of application. As a result, although their average performance is satisfactory, they might be inappropriate in some specific application domains. In this article, we study the case of detecting neighbors between large rigid molecules, which has applications in, e.g., rigid body molecular docking, Monte Carlo simulations of molecular self-assembly or diffusion, and rigid body molecular dynamics simulations. More precisely, we compare the traditional grid-based algorithm to a series of hierarchy-based algorithms that use bounding volumes to rapidly eliminate large groups of irrelevant pairs of atoms during the neighbor search. We compare the performance of these algorithms based on several parameters: the size of the molecules, the average distance between them, the cutoff distance, as well as the type of bounding volume used in the culling hierarchy (AABB, OBB, wrapped, or layered spheres). We demonstrate that for relatively large systems (> 100,000 atoms) the algorithm based on the hierarchy of wrapped spheres shows the best results and the traditional grid-based algorithm gives the worst timings. For small systems, however, the grid-based algorithm and the one based on the wrapped sphere hierarchy are beneficial.
authors: NANO-D, INRIA Grenoble - Rhone-Alpes Research Center, 38334 Saint Ismier Cedex, Montbonnot, France. svetlana.artemova@inria.fr
authors: Svetlana
authors: S
authors: Artemova
authors: Sergei
authors: S
authors: Grudinin
authors: Stephane
authors: S
authors: Redon
mesh_terms: D000465:Algorithms; D000818:Animals; D001052:Apoferritins / Q000737:chemistry / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D001820:Bluetongue virus / Q000737:chemistry / Q000378:metabolism; D036022:Capsid Proteins / Q000737:chemistry / Q000378:metabolism; D004058:Diffusion; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000378:metabolism; D006736:Horses; D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D012260:Ribonucleases / Q000737:chemistry / Q000378:metabolism; D013302:Streptomyces / Q000737:chemistry / Q000201:enzymology
chemical_list: D001426:Bacterial Proteins; D036022:Capsid Proteins; D004791:Enzyme Inhibitors; D011506:Proteins; C057438:barstar protein, Bacillus amyloliquefaciens; D001052:Apoferritins; D012260:Ribonucleases; C077002:ribonuclease Sa3