A Grid Service based Parallel Molecular Surface Reconstruction System

D’Agostino, Daniele; Clematis, Andrea; Merelli, Ivan; Milanesi, Luciano; Coloberti, M.

doi:10.1109/pdp.2008.54

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Molecular Surface and Mesh Generation1

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Cited by 2 publications

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“…Such calculation requires remeshing or mesh update at each time step. A main approach to dealing with the efficiency issue is to design and develop parallel mesh generation tools and PB solvers; see the work from D'Agostino et al [21].…”

Section: Molecular Surface and Mesh Generationmentioning

confidence: 99%

Mathematical and Numerical Aspects of the Adaptive Fast Multipole Poisson-Boltzmann Solver

Zhang

Cheng

et al. 2013

Commun. comput. phys.

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This paper summarizes the mathematical and numerical theories and computational elements of the adaptive fast multipole Poisson-Boltzmann (AFMPB) solver. We introduce and discuss the following components in order: the Poisson-Boltzmann model, boundary integral equation reformulation, surface mesh generation, the nodepatch discretization approach, Krylov iterative methods, the new version of fast multipole methods (FMMs), and a dynamic prioritization technique for scheduling parallel operations. For each component, we also remark on feasible approaches for further improvements in efficiency, accuracy and applicability of the AFMPB solver to large-scale long-time molecular dynamics simulations. The potential of the solver is demonstrated with preliminary numerical results.

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Section: Molecular Surface and Mesh Generationmentioning

confidence: 99%