Parallel AFMPB solver with automatic surface meshing for calculation of molecular solvation free energy. We present PAFMPB, an updated and parallel version of the AFMPB software package for fast calculation of molecular solvation-free energy. The new version has the following new features: (1) The adaptive fast multipole method and the boundary element methods are parallelized; (2) A tool is embedded for automatic molecular VDW/SAS surface mesh generation, leaving the requirement for a mesh file at input optional; (3) The package provides fast calculation of the total solvation-free energy, including the PB electrostatic and nonpolar interaction contributions. PAFMPB is implemented in C and Fortran programming languages, with the Cilk Plus extension to harness the computing power of both multicore and vector processing. Computational experiments demonstrate the successful application of PAFMPB to the calculation of the PB potential on a dengue virus system with more than one million atoms and a mesh with approximately 20 million triangles.
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References in zbMATH (referenced in 5 articles , 1 standard article )
Showing results 1 to 5 of 5.
- Quan, Chaoyu; Stamm, Benjamin; Maday, Yvon: A domain decomposition method for the Poisson-Boltzmann solvation models (2019)
- Fang, Fuhui; Huang, Jingfang; Huber, Gary; McCammon, J. Andrew; Zhang, Bo: Hierarchical orthogonal matrix generation and matrix-vector multiplications in rigid body simulations (2018)
- Liu, Tiantian; Chen, Minxin; Lu, Benzhuo: Efficient and qualified mesh generation for Gaussian molecular surface using adaptive partition and piecewise polynomial approximation (2018)
- Zhang, Bo; Huang, Jingfang; Pitsianis, Nikos P.; Sun, Xiaobai: RECFMM: recursive parallelization of the adaptive fast multipole method for Coulomb and screened Coulomb interactions (2016)
- Zhang, Bo; Peng, Bo; Huang, Jingfang; Pitsianis, Nikos P.; Sun, Xiaobai; Lu, Benzhuo: Parallel AFMPB solver with automatic surface meshing for calculation of molecular solvation free energy (2015)