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8.2 PBE Data Structures

In order to understand the function of the commands which use the Poisson-Boltzmann equation, it is important to know the underlying data structures.

The primary data structure is the pbe_info data structure, defined in the file, $CGS/pbe.h. This data structures contains the grids for the potential, charge density, dielectric constant, and Debye-Huckel parameter, kappa_bar. There are three grids stored for the dielectric constant because values for the dielectric constant are stored for the lines connecting grid points. Since there are three perpendicular lines connecting grid points to their neighbors, there are three dielectric constant grids, for the x, y, z directions. The epsx grid stores the dielectric constant for the midpoint of the line pointing in the x direction between grid points. The value of epsx[i,j,k] corresponds to the dielectric constants between grid points [i,j,k] and [i+1,j,k]. The value of epsy[i,j,k] corresponds to the dielectric constants between grid points [i,j,k] and [i,j+1,k], and the value of epsz is analagous for the the third indices, respectively. One two-dimensional cross section of each grid is unused.

The pbe_info data structure also contains the spatial origin of the grid, dimensions, and grid size so that the grid can be laid out over the space of the molecule of interest. It also contains a list of atoms included in the grid as well as their positions, radii, and charges. Finally, it contains a number of parameters which control the calculation.

The PBE SETUP command is used to setup this data structure. After the first PBE SETUP, the REUSE option controls whether the data structure is initialized or updated, see PBE SETUP Command.

It is important to remember that this data structure is not automatically updated when the coordinates change (except in the context of a conformational search).

It is possible to generate multiple pbe_info data structures, and to do operations on them. This is useful for comparing results generated by different methods or parameters.