Modelling of internal degrees of freedom, usual techniques:
V s t r ( r 12 ) = 1 2 K s t r ( r 12 − b 0 ) 2 {\displaystyle V_{str}(r_{12})={\frac {1}{2}}K_{str}(r_{12}-b_{0})^{2}}
Bond sequence: 1-2-3:
Bond Angle: θ {\displaystyle \theta }
cos θ = r → 21 ⋅ r → 23 | r → 21 | | r → 23 | {\displaystyle \cos \theta ={\frac {{\vec {r}}_{21}\cdot {\vec {r}}_{23}}{|{\vec {r}}_{21}||{\vec {r}}_{23}|}}}
Two typical forms are used to model the bending potential:
V b e n d ( θ ) = 1 2 k θ ( θ − θ 0 ) 2 {\displaystyle V_{bend}(\theta )={\frac {1}{2}}k_{\theta }\left(\theta -\theta _{0}\right)^{2}}
V b e n d ( cos θ ) = 1 2 k c ( cos θ − c 0 ) 2 {\displaystyle V_{bend}(\cos \theta )={\frac {1}{2}}k_{c}\left(\cos \theta -c_{0}\right)^{2}}
