AFMPB: An adaptive fast multipole Poisson Boltzmann solver for calculating electrostatics in biomolecular systems
- ORNL
A Fortran program package is introduced for rapid evaluation of the electrostatic potentials and forces in biomolecular systems modeled by the linearized Poisson-Boltzmann equation. The numerical solver utilizes a well-conditioned boundary integral equation (BIE) formulation, a node-patch discretization scheme, a Krylov subspace iterative solver package with reverse communication protocols, and an adaptive new version of fast multipole method in which the exponential expansions are used to diagonalize the multipole-to-local translations. The program and its full description, as well as several closely related libraries and utility tools are available at http://mccammon.ucsd.edu/. This paper is a brief summary of the program: the algorithms, the implementation and the usage.
- Research Organization:
- Oak Ridge National Laboratory (ORNL)
- Sponsoring Organization:
- USDOE
- DOE Contract Number:
- AC05-00OR22725
- OSTI ID:
- 981807
- Journal Information:
- Computer Physics Communications, Journal Name: Computer Physics Communications Journal Issue: 6 Vol. 181; ISSN 0010-4655
- Country of Publication:
- United States
- Language:
- English
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