1. Model frame

Molecular dynamics simulations are carried out on an isolated macromolecule or macromolecular complex. On a scale of a few nanometers, a solution or solid is represented by the set of coordinates of its component atoms, so that the trajectories of these coordinates over time can be simulated using a computer. Molecular dynamics simulation methods were developed in theoretical liquid physics in the 1980s [37] , and while effectively simulating only one copy of the macromolecule or macromolecular complex under study, they enable the study of all similar macromolecules present in the same solution. This is possible, subject to a number of assumptions that will be detailed in the following.

One of the aims of molecular modeling is to compare the energies of the conformers of a molecule. The most rigorous...