Parallel AFMPB solver with automatic surface meshing for calculation of molecular solvation free energy

Published: 1 January 2015| Version 1 | DOI: 10.17632/gm5zh6gxh7.1
Bo Zhang, Bo Peng, Jingfang Huang, Nikos P. Pitsianis, Xiaobai Sun, Benzhuo Lu


This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018) Abstract 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, incl... Title of program: Parallel AFMPB Catalogue Id: AEGB_v2_0 Nature of problem Numerical solution of the linearized Poisson-Boltzmann equation that describes electrostatic interactions of molecular systems in ionic solutions. Versions of this program held in the CPC repository in Mendeley Data AEGB_v1_0; AFMPB: Adaptive Fast Multipole Poisson-Boltzmann Solver; 10.1016/j.cpc.2010.02.015 AEGB_v1_1; AFMPB; 10.1016/j.cpc.2013.05.012 AEGB_v2_0; Parallel AFMPB; 10.1016/j.cpc.2014.12.022



Molecular Biology, Biological Sciences, Computational Physics