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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 section 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 section Generation of 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 section Minimization and Dynamics. When two calculations are being compared in the analysis facility, hydrogen bonds may be generated, see section 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 section Symmetry and Molecular 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).
HBONd hbond-spec
hbond-spec ::= [DUMMy] [CUTHB real] [CUTHBA real]
[CTONHB real] [CTOFHB real] [CTONHA real] [CTOFHA real]
Note: this syntax is also used in the HBUILD command, see section Purpose of the Coordinate Manipulation Commands, for more information.
Variable Default Function
DUMMy Sets CUTHB and CUTHBA to zero. This will result
in no hydrogen bonds which is desirable when one
is not interested in the hydrogen bond energy.
The selection will be done very quickly in this
case.
CUTHB 4.5 Maximum distance allowed for a hydrogen bond. This
distance is measured between the heavy atoms
CTOFHB CUTHB-0.5 Distance where distance switching function is off
Once specified, it will only change if respecified.
CTONHB CTOFHB-0.5 Distance where distance switching function is on.
Once specified, it will only change if respecified.
CUTHBA 90.0 Maximum out of line angle allowed for a three
atom hydrogen bond. The angle is 180 - D--H...A angle.
If this value is less than or equal to 0,
then all possible angles will be allowed.
CTOFHA CUTHBA-20.0 Angle where angle switching function is off
Once specified, it will only change if respecified.
CTONHA CTOFHA-20.0 Angle where angle switching function is on.
Once specified, it will only change if respecified.
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