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