8.2.2.1 The stretch energy

In the AMBER force field there are three terms describing the interactions between atoms that are either directly bonded or separated by two or three bonds. These three terms are known as the bonded terms and correspond to bonds, angles, and dihedrals, respectively. The first term (Kr(r — req)2) describes a simple harmonic potential obeying Hooke’s law and is used to represent the energy involved in the stretching of a bond between two directly linked atoms. 2Kr is the force constant for the bond and (r — req) the distortion from the equilibrium bond length. It should be immediately obvious from this expression that such an approach prohibits the study of bond breaking since the expression tends to infinity as the bond length is increased significantly beyond the equilibrium value.

The harmonic representation of the potential is the simplest possible but provides a fair description of the energetics of bond stretching and compression when the bond length remains close to the equilibrium value (Figure 8.1). While more complex descriptions are available they come at the price of increased computational complexity and increased pa­rameterization requirements and are rarely used for modeling biological systems.