10.4.1 Specifying Distance Limits for Nonbonded Contacts

Distance limits for nonbonded contacts can be defined in two ways:

As absolute values in Angstroms, e.g. 2 < d(X...Y) < 5Å.
As distances relative to the sum of van der Waals Radii, i.e.

v(X) + v(Y) - p < d(X...Y) < v(X) + v(Y) - q

where v(X) and v(Y) are the vdW radii of X and Y respectively and p and q are user-specified values in Angstrom (e.g. if p = 0.5 and q = 0.1, the contact must be at least 0.1Å shorter than the sum of vdW radii but no more than 0.5Å shorter).

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