The intramolecular interaction energy is the summation of the individual
nonbonded interaction energies for pairs of atoms within the current
molecular
structure, e.g., a single molecule or a crystallographic asymmetric unit.
The computational time is further reduced by introducing an approximation, storing the atomic pair indices () that satisfy in a list that is updated only when any atom has moved more than the amount specified by TOLErance. For both switched and shifted nonbonded options (see Section 3.2.1), the distance at which the energy becomes zero is given by . Thus, the nonbonded energy calculations become independent of the update frequencies if .
There are a number of cases for nonbonded interactions that must not be computed, e.g., interactions between covalently bonded atoms. Covalently bonded exclusions are automatically generated by X-PLOR using information about atom connectivity. In addition, certain exclusions can be added manually by the EXCLude statement, which is an atom statement (see Section 3.1.1). The NBXMod statement (see Section 3.2.1) has several options for automatically excluding 1-2, 1-2 and 1-3, and 1-2, 1-3, and 1-4 interactions in the molecule. In the case of NBXMod=5, the 1-4 interactions are treated in a special way. The electrostatic 1-4 interactions are scaled by , and the van der Waals interactions use a special 1-4 set of parameters for and . In the case of NBXMod5, 1-4 interactions are treated as normal nonbonded interactions, and the second terms of the right-hand side of Eqs. 4.17 and 4.18 become zero.
Xplor-NIH 2023-11-10