ION calculates the distribution of ions around biomolecules, especially highly charged nucleic acids. The molecules and ions are modeled explicitly and represented by atomic partial charges and radii, and the solvent is modeled implicitly as a continuum medium. The distribution of the electrostatic potential is a solution of the Dirichlet problem for the Poisson equation. The solution is generated for various ion configurations determined by applying the Metropolis Monte-Carlo algorithm. Therefore, with the ION program one can perform the Monte-Carlo dynamics accounting for the finite size of ions.
ION uses the PETSc package (http://www.mcs.anl.gov/petsc/petsc-as/) for calculating the solution of the Dirichlet problem for the Poisson equation in every iteration of the Mone-Carlo calculation. ION is fully parallelized with the MPI technology.
ION 2 (June 3, 2013):
See Changelog for updates and bug fixes.