The generation of hydrogen bonds is one of the major steps in evaluating the energy of a system. The process of hydrogen bond generation involves looking at all possible pairs of hydrogen bond donors and acceptors and selecting those which are "good". The meaning of "good" is determined by parameters to be described below. Depending on the setting of the H-A or D-A flags in the parameter file, see Parameter File Format, hydrogen bonds can involve either two or three atoms, respectively. Two atom hydrogen bonds will not have any angular term calculated.
The selection of hydrogen bonds involves several checks. First, any good hydrogen bond has be shorter than the distance cutoff, CUTHB. If the H-A parameter flag is set, hydrogen bond distances are measured from the hydrogen to the acceptor. If the D-A flag is set, hydrogen bond distances are measured from the heavy atom donor to the heavy atom acceptor. A second test involving the heavy atom donor, hydrogen, and acceptor applies for the three atom case. The angle off linearity has to be less than the angular cutoff, CUTHBA. This angle is measured as the complement of donor - hydrogen - acceptor angle. Thus, a linear hydrogen bond would be measured as a zero angle. In all cases, hydrogen bonds are not calculated for any set of atoms where any pair of atoms are excluded from non-bonded interactions. see Non-bonded Interactions.
Because there are cutoffs involved with the selection of hydrogen bonds, and because the hydrogen bond list must be updated during dynamics, and because energy must be conserved, switching functions are needed to smooth the transition over a cutoff. Therefore, the specification of hydrogen bond generation also allows the specification of switching function parameters.
The generation is performed by CONGEN at several different points. One can request the hydrogen bonds be generated explicitly using a hydrogen bond command. This is useful prior to analyzing the system. The hydrogen bonds can be generated during any energy manipulation, see Energy Manipulations. When two calculations are being compared in the analysis facility, hydrogen bonds may be generated, see Comparisons. When any such generation is requested except in the analysis facility, the same specifications are made for the hydrogen bond generation and switching function parameters.
If images are present (see Images) and the selection of image atoms has occurred, then all hydrogen bonds between primary atoms and image atom will also be generated. During dynamics or minimization, the image hydrogen bonds must be updated each time new image atoms are selected (in nonbonded update), thus there is a forced generation of image hydrogen bonds (unless the update frequencies match).