TABI-PB

TABI-PB (treecode-accelerated boundary integral) solves the linearized Poisson-Boltzmann equation. The solver employs a well-conditioned boundary integral formulation for the electrostatic potential and its normal derivative on a triangulated molecular surface, and the integral equations are discretized by nodepatch method. The linear system is solved by GMRES iteration, and the matrix-vector product is carried out by a barycentric Lagrange interpolation dual tree traversal (BLDTT) fast summation method which reduces the cost from O(N^2) to O(N), where N is the number elements. This solver also includes NVIDIA GPU support using OpenACC with the PGI/ NVIDIA HPC compilers.

This TABI-PB repo serves as a submodule to APBS, and also works as a standalone distribution. For more information on building APBS, visit this link.

Authors:

Leighton W. Wilson (lwwilson@umich.edu)
Robert Krasny (krasny@umich.edu)
Weihua Geng (wgeng@smu.edu)
Jiahui Chen (chenj159@msu.edu)

References

Please refer to the following references for more background:

E. Jurrus, D. Engel, K. Star, K. Monson, J. Brandi, L. E. Felberg, D. H. Brookes, L. Wilson, J. Chen, K. Liles, M. Chen, P. Li, D. W. Gohara, T. Dolinsky, R. Konecny, D. R. Koes, J. E. Nielsen, T. Head- Gordon, W. Geng, R. Krasny, G. W. Wei, M. J. Holst, J. A. McCammon, and N. A. Baker, Improvements to the APBS biomolecular solvation software suite, Protein Sci. 27 (2017), 112-128.
W.H. Geng and R. Krasny, A treecode-accelerated boundary integral Poisson-Boltzmann solver for continuum electrostatics of solvated biomolecules, J. Comput. Phys. 247 (2013), 62-87.
L. Wilson, W. Geng and R. Krasny, TABI-PB 2.0: An improved version of the Treecode-Accelerated Boundary Integral Poisson-Boltzmann solver, J. Phys. Chem. B 126 (2022), 7104-7113.

Build Instructions

This project uses CMake to manage and configure its build system. In principle, building an independent tabipb executable is as simple as executing the following from the top level directory of TABI-PB:

mkdir build; cd build; export CC=<CXX compiler>; cmake ..; make

This creates a tabipb executable located at TABI-PB/build/bin/tabipb. Compiling the GPU version requires that a PGI/ NVIDIA HPC C++ compiler be used, and that cmake be invoked with the flag -DENABLE_OPENACC=ON.

tabipb relies on NanoShaper to triangulate the molecular surface. To get a NanoShaper executable appropriate for your system, invoke cmake with the flag -DGET_NanoShaper=ON.

Examples

To run an example, navigate to the examples directory, and run tabipb with the example input file:

cd examples/
../build/bin/tabipb usrdata.in

License

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