Parallel higher-order boundary integral electrostatics computation on molecular surfaces with curved triangulation

JOURNAL OF COMPUTATIONAL PHYSICS

卷:241

Article

Geng, Weihua

关键词: Poisson-Boltzmann;    Electrostatics;    Boundary integral;    Parallel computing;    Message passing interface (MPI);   

DOI  :  10.1016/j.jcp.2013.01.029

来源: Elsevier

【 摘 要 】

In this paper, we present a parallel higher-order boundary integral method to solve the linear Poisson-Boltzmann (PB) equation. In our method, a well-posed boundary integral formulation is used to ensure the fast convergence of Krylov subspace linear solver such as GMRES. The molecular surfaces are first discretized with flat triangles and then converted to curved triangles with the assistance of normal information at vertices. To maintain the desired accuracy, four-point Gauss-Radau quadratures are used on regular triangles and sixteen-point Gauss-Legendre quadratures together with regularization transformations are applied on singular triangles. To speed up our method, we take advantage of the embarrassingly parallel feature of boundary integral formulation, and parallelize the schemes with the message passing interface (MPI) implementation. Numerical tests show significantly improved accuracy and convergence of the proposed higher-order boundary integral Poisson-Boltzmann (HOBI-PB) solver compared with boundary integral PB solver using often-seen centroid collocation on flat triangles. The higher-order accuracy results achieved by present method are important to sensitive solvation analysis of biomolecules, particularly when accurate electrostatic surface potentials are critical in the molecular simulation. In addition, the higher-order boundary integral schemes presented here and their associated parallelization potentially can be applied to solving boundary integral equations in a general sense. (C) 2013 Elsevier Inc. All rights reserved.

【 授权许可】

Free