Parallel AFMPB solver with automatic surface meshing for calculation of molecular solvation free energy
| Main Author: | CPC, Mendeley |
|---|---|
| Other Authors: | Zhang, Bo, Peng, Bo, Huang, Jingfang, Pitsianis, Nikos P., Sun, Xiaobai, Lu, Benzhuo |
| Format: | Dataset |
| Terbitan: |
Mendeley
, 2015
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| Subjects: | |
| Online Access: |
https:/data.mendeley.com/datasets/gm5zh6gxh7 |
Daftar Isi:
- 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