Molecular mechanics and force field

Molecular modeling is a useful tool for studying many interesting systems. However, systems that contain thousands of atoms are often too large to be studied using quantum mechanics methods, which focus on the behavior of electrons within a system. Molecular mechanics (MM) methods ignore the electronic motions and simulate the behavior of molecules based on classical mechanics principles, where the energy of a system is studied as a function of the nuclear positions only. It involves the use of force fields, which are mathematical models that describe the interactions between atoms and molecules. Force fields are typically constructed by assigning parameters to the different types of atoms and bonds in a molecule. These parameters define the strength and directionality of the various interatomic forces, such as electrostatic, van der Waals, and covalent bonding interactions. The force field parameters are derived from experimental data, quantum mechanical calculations, and other sources of information. Once the force field is constructed, it can be used to calculate the potential energy and forces of a molecule, which can be used to predict its structure, stability, and dynamics. MM is used extensively in computational chemistry and drug discovery. Additionally, it is often used to study the properties and behavior of large biomolecules such as proteins and nucleic acids. To study the behavior of molecules that contain over thousands of atoms, molecular mechanics are widely applied using classical mechanics principles to describe the interactions between atoms and molecules. This chapter presents an overview of general empirical force fields applied to biological systems in multiscale molecular modeling from all-atom to coarse-grained models, including the polarizable model for molecules that involve significant polarizability.