Coarse Grained Go Models

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Introduction
In previous sections, especially the one describing the energy function, we have implicitly assumed a representation of the molecular system in which each atom is described as a single point that may be connected via bonds to other points (atoms). The force acting on an atom is the sum of that caused by these bonds as well as non-bonded interactions (electrostatics, van der Waals). However, this is only one way that a molecular system can be described, Quantum chemistry software packages, for example, calculate energy based on the wave functions (representing the electron densities) of the system's atoms. Depending on exactly how this is done, this can be many orders of magnitude more computationally expensive than calculating classical energy and forces. It is also possible to construct a potential energy function that is much cheaper to calculate, and that is what will be discussed in this section of the tutorial.

In particular, we will discuss