Potential energy function for proteins

We talked on van der Waals interactions and hydrophobic collapse. Here we provide a complete set of the different energy terms that are found proteins. Note that we are thinking on proteins as one-dimensional chains. There is a need to describe correctly the covalent (bonded) interaction between the chain as well as the non-bonded interactions.

The energy function is a sum of two body, three body, and four body terms. The three and four body terms are found only in the covalent part and two body terms are found in the covalent and non-bonded parts.

Which of the terms above is the most expensive to compute?