Nonbonded interactions (frequently abbreviated NBONDS) refer to all those terms in the hamiltonian which do not refer specifically to a bond, bond angle, dihedral, or hydrogen bond. They include the attractive and repulsive van der Waals terms and the electrostatic terms between all atom pairs that are not specifically excluded from nonbond calculations. Directly bound atoms (1-2 interactions) and atoms bound to a common atom (1-3 interactions) are usually not counted in non-bonded interactions. See Nbxmod, for an automated command to handle non-bonded exclusions. These terms are defined on atom pairs and to a first approximation would require the number of atoms squared calculations. To avoid this burden, various truncation and approximation schemes can be employed in the program, breaking the nonbonded calculation into two parts, initialization and actual energy calculation.
The method of approximation, cutoffs, and other relevant parameters can be entered either at the time of initialization (by calling NBOND from the main program or in the COMPARE command in analysis), or in the MINI and DYNA commands.