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- W2048574808 abstract "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 thedistributive 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." @default.
- W2048574808 created "2016-06-24" @default.
- W2048574808 creator A5032088629 @default.
- W2048574808 creator A5083674798 @default.
- W2048574808 date "2010-12-03" @default.
- W2048574808 modified "2023-10-18" @default.
- W2048574808 title "Exploring a coarse-grained distributive strategy for finite-difference Poisson–Boltzmann calculations" @default.
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- W2048574808 doi "https://doi.org/10.1007/s00894-010-0904-4" @default.
- W2048574808 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/3143316" @default.
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