Discussing the Angle and angle/harmonic classes
In this section, we will study the Angle class and demonstrate a typical angle-dependent potential, as implemented by the angle/harmonic child class.
An angle-dependent potential is a form of intramolecular potential present among bonded atoms. An angle that's formed by a chain of three bonded atoms can exert forces on those three atoms based on the deviation of this angle from an equilibrium value.
Given an angle-dependent potential, 
, we can calculate the force on each atom using the procedure presented. The following diagram shows a chain of three bonded atoms (1, 2, 3) with (
), (
), and (
) coordinates, respectively, that form an angle, 
:
Figure 8.18 – An angle, 
, formed by three bonded atoms – 1,2,3
As you can see, the, 
bond vector that points from atom 2 to atom 1 is formulated as follows:
Similarly, the 
bond vector that points from atom 2 to atom 3 is...
