Exploring a coarse-grained distributive strategy for finite-difference Poisson–Boltzmann calculations
| Autor: | Meng-Juei Hsieh, Ray Luo |
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| Jazyk: | angličtina |
| Předmět: |
Models
Molecular Finite difference Computer science Static Electricity 010402 general chemistry Topology 01 natural sciences Catalysis Inorganic Chemistry Medicinal and Biomolecular Chemistry Dimension (vector space) Computational chemistry Models Poisson-Boltzmann Theoretical and Computational Chemistry Computer cluster 0103 physical sciences Domain decomposition Physical and Theoretical Chemistry Block (data storage) Original Paper Poisson–Boltzmann Chemical Physics 010304 chemical physics Electrostatic focusing Organic Chemistry Computational Biology Molecular Domain decomposition methods Poisson–Boltzmann equation Grid 0104 chemical sciences Computer Science Applications Distributive property Computational Theory and Mathematics Algorithms Distributive computing Physical Chemistry (incl. Structural) |
| Zdroj: | Journal of molecular modeling, vol 17, iss 8 Journal of Molecular Modeling |
| ISSN: | 1610-2940 |
| DOI: | 10.1007/s00894-010-0904-4 |
| Popis: | We have implemented and evaluated a coarse-grained distributive method for finite-difference Poisson-Boltzmann (FDPB) calculations of large biomolecular systems. This method is based on the electrostatic focusing principle of decomposing a large fine-grid FDPB calculation into multiple independent FDPB calculations, each of which focuses on only a small and a specific portion (block) of the large fine grid. We first analyzed the impact of the focusing approximation upon the accuracy of the numerical reaction field energies and found that a reasonable relative accuracy of 10(-3) can be achieved when the buffering space is set to be 16 grid points and the block dimension is set to be at least (1/6)(3) of the fine-grid dimension, as in the one-block focusing method. The impact upon efficiency of the use of buffering space to maintain enough accuracy was also studied. It was found that an "optimal" multi-block dimension exists for a given computer hardware setup, and this dimension is more or less independent of the solute geometries. A parallel version of the distributive focusing method was also implemented. Given the proper settings, the distributive method was able to achieve respectable parallel efficiency with tested biomolecular systems on a loosely connected computer cluster. |
| Databáze: | OpenAIRE |
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