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[Licence| Download | New Version Template] aegb_v2_0.tar.gz(2294 Kbytes)
Manuscript Title: Parallel AFMPB solver with automatic surface meshing for calculations of molecular solvation free energy
Authors: Bo Peng, Bo Zhang, Jingfang Huang, Nikos P. Pitsianis, Xiaobai Sun, Benzhuo Lu
Program title: Parallel AFMPB
Catalogue identifier: AEGB_v2_0
Distribution format: tar.gz
Journal reference: Comput. Phys. Commun. 190(2015)173
Programming language: Mixed C and Fortran, Compiler: Intel or GNU with Cilk Plus enabled.
Computer: Any, but the code is mainly designed for multicore architectures.
Operating system: Linux.
RAM: Depends on the size of the discretized biomolecular system.
Keywords: Poisson-Boltzmann equation, Boundary integral equation, Auto- matic surface meshing, Solvation free energy, Fast multipole methods, Paralleliza- tion, Cilk.
PACS: 02.70.Ns, 02.70Pt, 41.20.Cv, 87.14.E-.
Classification: 3.

External routines: Users are allowed to use external routines/libraries (e.g., MSMS [11] and TMSMesh [4]) to generate compatible surface mesh input data if they choose not to use the embedded automatic mesh generation tool in the package. Post-processing tools such as VCMM [7] and VMD [3] can also be used for visualization and analyzing results.

The package uses two subprogram: (1) The iterative Krylov subspace solver, SPARSKIT, from Yousef Saad [2]; and (2) Cilk-based parallel fast multipole methods from FMMSuite [1].

Does the new version supersede the previous version?: No

Nature of problem:
Numerical solution of the linearized Poisson-Boltzmann equation that describes electrostatic interactions of molecular systems in ionic solutions.

Solution method:
The linearized Poisson-Boltzmann equation is reformulated as a boundary integral equation and is subsequently discretized using the node- patch scheme. The resulting linear system is solved using Krylov subspace solvers iteratively. The reformulation of the equation provides an upper bound for the number of iterations. Within each iteration, the matrix-vector multiplication is accelerated using the adaptive plane-wave expansion based fast multipole methods. The majority of the codes are parallelized using the Cilk runtime.

Reasons for new version:
The force calculations in the previous version are deleted.

Summary of revisions:
The computation is parallelized and an automatic mesh generation method for BEM is added.

Restrictions:
The program has only been tested on machines running Linux operating system.

Additional comments:
The Cilk runtime used in the development and testing is from the Intel compiler Suite. The GNU Cilk Plus and Cilk Plus/LLVM branches have not been tested.

Running time:
The running time depends on the number of discretized elements (N) and their distribution. It also depends on the number of cores used in the computation.

References:
[1] http://www.fastmultipole.org/.
[2] http://www-users.cs.umn.edu/~saad/software/.
[3] http://www.ks.uiuc.edu/Research/vmd/.
[4] www.continuummodel.org.
[5] S. Bai, B. Lu, VCMM: A visual tool for continuum molecular modeling. J. Mol. Graph. Model. 50(2014) 44-49.
[6] N.A. Baker, D. Sept, S. Joseph, Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98(2001) 10037-10041.
[7] Scanner, F. Michel, Olson, J. Arthur, Spehner, J. Claude, Reduced surface: An efficient way to compute molecular surfaces. Biopolymers 38(1996) 305-320.