PAFMPB
swMATH ID:  16770 
Software Authors:  Zhang, Bo; Peng, Bo; Huang, Jingfang; Pitsianis, Nikos P.; Sun, Xiaobai; Lu, Benzhuo 
Description:  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 solvationfree 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 solvationfree 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. 
Homepage:  http://cpc.cs.qub.ac.uk/summaries/AEGB_v2_0.html 
Keywords:  PoissonBoltzmann equation; boundary integral equation; automatic surface meshing; solvation free energy; fast multipole methods; parallelization; Cilk Plus 
Related Software:  tabipb; TMSmesh; AFMPB; APBS; VCMM; DASHMM; TABI; MIBPB; RECFMM; Cilk; DAFMPB; PyGBe; PBEQSolver; UHBD; DelPhi; SMPBS; SDPBS; GTEngine; SIMS; MetaMol 
Referenced in:  6 Publications 
Standard Articles
1 Publication describing the Software, including 1 Publication in zbMATH  Year 

Parallel AFMPB solver with automatic surface meshing for calculation of molecular solvation free energy. Zbl 1344.78004 Zhang, Bo; Peng, Bo; Huang, Jingfang; Pitsianis, Nikos P.; Sun, Xiaobai; Lu, Benzhuo 
2015

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Referenced by 18 Authors
Referenced in 3 Serials
3  SIAM Journal on Scientific Computing 
2  Communications in Computational Physics 
1  Computer Physics Communications 
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