Fast Adaptive Computation of Neighbouring Atoms

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The main cost of a molecular dynamics or Monte Carlo simulation is the computation of the current potential energy or forces resulting from the interaction of atoms composing the molecular system. When a distance cut-off is used to speed up this computation, a fast method is needed to determine pairs of neighbouring atoms. We have recently introduced an adaptive torsion-angle quasi-statics simulation algorithm. Our adaptive algorithms enable a user to finely trade between precision and computational cost, while providing some precision guarantees [Rossi et al. 2007]. In this talk, we present a novel algorithm to efficiently determine pairs of neighbouring atoms, which takes advantage of the adaptivity of the simulation to speed up the computations, resulting in potentially large speedups when few degrees of freedom are active. R. Rossi, M. Isorce, S. Morin, J. Flocard, K. Arumugam, S. Crouzy, M. Vivaudou, and S. Redon. “Adaptive torsion-angle quasi-statics: a general simulation method with applications to protein structure analysis and design”. Bioinformatics 2007 23(13):i408-i417

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Journal: TechConnect Briefs
Volume: 3, Nanotechnology 2008: Microsystems, Photonics, Sensors, Fluidics, Modeling, and Simulation – Technical Proceedings of the 2008 NSTI Nanotechnology Conference and Trade Show, Volume 3
Published: June 1, 2008
Pages: 721 - 724
Industry sector: Advanced Materials & Manufacturing
Topics: Informatics, Modeling & Simulation
ISBN: 978-1-4200-8505-1