The switching function SW maintains a continuous and smooth function to the cutoff point so that derivatives are well defined at the cutoff point. The sum in Eq. 4.25 extends over all pairs of donors and acceptors (DONOr and ACCEptor statements; see Section 3.1.1) for which the donor-acceptor distance and the donor-hydrogen-acceptor angle satisfy the criteria specified by DCUT and ACUT (see Section 3.2.1). AEXP assigns the exponent, REXP assigns the exponent, HAEX assigns the exponent, and AAEX assigns the exponent; and are defined by the HBON statement (see Section 3.2.1). The remaining switching parameters are provided by the hbonds statement. The computational time for searching for hydrogen bonds that satisfy the cutoff criteria is reduced by introducing an approximation, storing the atomic pair indices () that satisfy the cutoff criteria in a list that is updated only when any atom has moved more than the value specified by TOLErance.
Xplor-NIH 2023-11-10