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18 Comparisons

The COMPARE command is used to specify that a comparison is to be performed. The comparison may be done within the current calculation or may be done with a different PSF, a different coordinate set, a different parameter set, a different hydrogen bond list, a different non-bonded list, a different set of constraints, a different set of averaging data structures, a different Poisson-Boltzmann data structure or any combination thereof. In addition, the COMPARE command can be used to reorient an entire coordinate trajectory with respect to a reference coordinate set.

Before one uses the COMPARE command, it is important to understand what the the program needs to do a comparison. When the analysis facility is called, it needs at least seven data structures; a PSF, a coordinate set, a set of harmonic constraints, a parameter set, a parameter coding set, hydrogen bond list, and a non-bonded list. It may also require the Poisson-Boltzmann data structure or one of dynamical average data structures. The function of the COMPARE command is to create another set of these seven data structures to be used for comparison calculations, and to establish a relationship between the two sets of data structures. Let us examine each of these tasks in turn.

The creation of the comparison data structures is a very straightforward operation. The COMPARE command allows one to specify Fortran unit numbers which refer to binary files for the comparison PSF, coordinate set, harmonic constraints, parameter set, hydrogen bond list, and non-bonded list. The parameter coding list is generated without user intervention. In addition, the user may generate a new hydrogen bond list or non-bonded list with different selectional rules than were used in the main calculation.

If a user does not specify how to create a particular data structure, the data structures are taken from the main calculation (in the case of the PSF, constraints, coordinates, and parameters) or generate them using parameters as specified in the main calculation (the case for the hydrogen bond and non-bonded list). In addition, if any dynamical averaging data structures or Poisson-Boltzmann data structures have been created and the comparison PSF is the same as the main, then the comparison dynamical averaging data structures and Poisson-Boltzmann data structures will be assigned to those of the main.

The relating of the two calculations is more involved. Basically, if one has a pairing between the atoms in the main PSF and the atoms in the comparison PSF, it is possible to relate any internal coordinate or hydrogen bond. This pairing is generated in a three step process where we first match segments, then residues, and finally atoms — mirroring the hierarchy of organization used in the PSF.