Atomic coordinates difference function

A force field does not consist only of a mathematical eiqjression that describes the energy of a molecule with respect to the atomic coordinates. The second integral part is the parameter set itself. Two different force fields may share the same functional form, but use a completely different parameterization. On the other hand, different functional forms may lead to almost the same results, depending on the parameters. This comparison shows that force fields are empirical there is no "correct form. Because some functional forms give better results than others, most of the implementations within the various available software packages (academic and commercial) are very similar. 

The order parameter can be defined in two different ways. It can be either a function of atomic coordinates or just a parameter in the Hamiltonian. Examples of both types of order parameters are given in Sect. 2.8.1 in Chap. 2 and illustrated in Fig. 2.5. This distinction is theoretically important. In the first case, the order parameter is, in effect, a generalized coordinate, the evolution of which can be described by Newton s equations of motion. For example, in an association reaction between two molecules, we may choose as order parameter the distance between the two molecules. Ideally, we often would like to consider a reaction coordinate which measures the progress of a reaction. However, in many cases this coordinate is difficult to define, usually because it cannot be defined analytically and its numerical calculation is time consuming. This reaction coordinate is therefore often approximated by simpler order parameters. 

As an example, the structure of the CsCl-type has been discussed by Carter using several criteria of evaluation of At. In a geometrical approach a weighted coordination number as a function of atomic radii difference was described. 

All of the likely conformations of cellobiose, cellulose, and xylan are explored systematically assuming the ring conformations and IC-D-O-IC-4 ) angle for each pair of residues to be fixed and derivable from known crystal structures. The absolute van der Waals energies, but not the relative energies of different conformations, are sensitive to the choice of energy functions and atomic coordinates. The results lead to possible explanations of the known conformational stiffness of cellulose and Its solubility properties in alkali. The characteristics of xylan conformations are compared with cellulose. 

Of these, types (i), (ii) and (iii) are most common. Type (iv) is rare and implies sp2, rather than sp, hybridisation at the N atom. Thiocyanate is described as an ambidentate ligand, being able to coordinate via either or both of two atoms of different atomic number. It is not, however, a chelating ligand a bidentate function would require that the lone pairs on both N and S point to the same central atom, which is not feasible. Other... 

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