Bonds

Bonds describe a linear bond between two atoms. These bonds are described by simple harmonic springs. The energy of a bond between atoms i and j is given by

$$E_{\text{bond}} = k{(\vert{\vec{r}}_{ij}\vert - r_0)}^2$$

where

• k = spring constant specified in the parameter file for this bond type
• $\vert\vec{r}_{ij}\vert$ = calculated distance between atoms i and j
• r₀ = rest distance of the bond specified in the parameter file for this bond type