Programs in Physics & Physical Chemistry
|[Licence| Download | New Version Template] adit_v1_0.tar.gz(241 Kbytes)|
|Manuscript Title: Solutions of Poisson's equation in channel-like geometries.|
|Authors: M. Hoyles, S. Kuyucak, S.-H. Chung|
|Program title: bics|
|Catalogue identifier: ADIT_v1_0|
Distribution format: tar.gz
|Journal reference: Comput. Phys. Commun. 115(1998)45|
|Programming language: Fortran.|
|Computer: Fujitsu VPP300.|
|Operating system: UNIX.|
|RAM: 720M words|
|Word size: 32|
|Keywords: Biology, Poisson's equation, Ion channels.|
Nature of problem:
The program calculates the potential energy of and force on an ion in the vicinity of a model ion channel. It can include the effects of an externally applied field and fixed charges other than the ion. It can also calculate the electric field and potential in the absence of an ion.
We treat ions and fixed charges as point charges, and treat water and channel protein as regions of constant dielectric strength. The electric potential at a point in the pore can be found by solving Poisson's equation with appropriate boundary conditions. The program uses one of two methods. The iterative method distributes a grid of surface charges across an arbitrary cylindrically symmetric boundary, and modifies them iteratively until it finds a self-consistent solution. The analytical method computes a finite number of terms in an infinite series which is a solution to Poisson's equation for a toroidal boundary.
The program takes advantage of the new features of Fortran 90. It is split into modules rather than subroutines, and uses the concept of abstract data types to regulate data structures.
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