Molecular modelling bond torsion energy

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Rotation about the central bond costs energy and there are two components to this one arises from the repulsion between the first and fourth atoms in the sequence and the other is intrinsic to the bond. The former component is included in the nonbonded interactions of the molecular mechanics model but the other component must be explicitly included by means of a torsion angle potential energy function. 

Molecular modeling using either Monte-Carlo simulations or molecular dynamics is used to apply molecular mechanics energy minimizations to very complex systems [348]. In complex flexible molecules such as proteins or nucleic adds, the number of variable parameters, i.e., bond torsion angles, is such that the global search for energy minima becomes impossible The same problem occurs with theoretical calculations of water structure in aqueous solutions or in heavily hydrated crystals. 

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