Potential Energy and Molecular Thermodynamics

The problem in trying to model the 3D structure of a biomacromolecular is formidable because of the large size and complexity of the system and therefore some simplifications and assumptions are required  

Molecular mechanics The accurate predictions of the structure and physical properties for a molecule can be made from an exact quantum mechanical treatment of every atom within the molecular system. However, a simpler molecular mechanical treatment is applied to solve a complex macromolecular system. 

Energy minimum The native conformation of a macromolecule is the one with the lowest overall potential energy. Therefore energy minimization is applied to search for the native/most stable conformation of a biomacromolecule. 

In vacuo All the biomacromolecules function in solvent environments, but the complexity of the system is greatly reduced in vacuo by removing all the solvent and ions. Various approximations (e.g. bulk dielectrics, periodic box) have been incorporated into the modeling methods to simulate solvent effects without explicitly including solvent molecules. 

Periodic box The properties of a population of molecules is represented by the time-average behavior of a single molecule and its associated solvent isolated in a 

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