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The Born ion is the canonical electrostatics example; a non-polarizable sphere embedded in a higher-dielectric medium. Due to the spherical symmetry of this example, analytical solutions exist for a number of observables. In this example, we're going to examine the change in polar solvation energy and electrostatic potential for Born ions of various radii.
First, we'll look at an example PQR file which provides the molecular information (coordinates, charges, and radii) to the electrostatics software. Everything an implicit solvent electrostatics software package needs to know about the molecule is specified here. The PQR file is simply a modified version of the standard PDB format. This means that PQR files can be read into most molecular visualization programs.
Example 1. Example PQR file
REMARK This is an ion with a 3 A radius and a +1 e charge
ATOM 1 I ION 1 0.000 0.000 0.000 1.00 3.00
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This example PQR file gives an ion located at (0, 0, 0) with a +1 e charge and a 3 A radius. It can be downloaded here and loaded into VMD with the command:
$ vmd -pdb ion.pqr
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