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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.