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A comparison of neighbor search algorithms for large rigid molecules
Author(s) -
Artemova Svetlana,
Grudinin Sergei,
Redon Stephane
Publication year - 2011
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.21868
Subject(s) - bounding volume , algorithm , grid , monte carlo method , computer science , bounding overwatch , hierarchy , computation , molecular dynamics , rigid body , series (stratigraphy) , mathematics , physics , computational chemistry , chemistry , geometry , collision detection , artificial intelligence , paleontology , statistics , computer security , classical mechanics , economics , market economy , biology , collision
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. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011