The surface of the molecule is constructed in the following way. The Gaussian function is assigned to each atomic center:
where the ra vector defines the position of atom a and Ra is a specific radius of atom a (as given in the pqr file). This Gaussian function has the following properties:
– at the nucleus center a its value is 2,
– at |ra – r| = Ra it equals to 1 (i.e. half of its maximum value).
The volume occupied by a molecule (or molecular density) is defined as a sum over all atoms, a:
The surface of the molecule is defined as the surface corresponding to the isovalue of 1. The figures shown below present the van der Waals surface of a molecule (left) and its molecular surface computed using atom-centered Gaussian functions (right).
The definition of the surface of the molecule used by Surface Diver can be modified with the [irad] parameter.