Question

Explain the general concept of a force field in molecular modelling and explain why it might be used instead of a first-principles method.

Answer 1

The force field in the molecular modeling is nothing but the algorithm which calculate or measure the potential energy (E) functions or interatomic potentials of a system of atoms or coarse-grained particles in molecular mechanics. It is derived from the experiments in combination with physics, chemistry and quantum mechanics.

The basic functional form of potential energy (E) in molecular mechanics includes bonded terms for interactions of atoms that are linked by covalent bonds, and nonbonded or noncovalent terms which describe the long-range electrostatic and van der Waals forces.

An atom force fields provide parameters for every type of atom in a system, including hydrogen, while united-atom interatomic potentials treat the hydrogen and carbon atoms as combined potential also known as coarse -grained potentials

The force field terms can be written as total potential energy (E _total)

E _totalE _bonded + E _nonbonded

Where the components of the covalent and noncovalent contributions are given by the following summations:

E _bondedE _bond + E _angle + E _dihyderal

E _nonbondedE _{Van der Waals} + E _{electrostatics}

The bond means the bond length, bond angle and dihyderal angle terms are usually modeled by quadratic energy functions that do not allow bond breaking and covalent bond provided with stretching potential. The functional form for dihedral energy is highly variable with the planarity of aromatic rings and conjugated systems.

The nonbonded terms are most computationally intensive. A popular choice is to limit interactions to pairwise energies. The van der Waals term is usually computed with a Lennard-Jones potential and the electrostatic term with Coulomb's law.

The force field is also the collection of equations and associated constants designed to reproduce molecular geometry and selected properties of tested structures.

Multiple force fields have been developed as on today, depending on their use and purpose.

Optimized Potential for Liquid Simulations (OPLS-2005 and OPLS-3) useful for the protein molecular modeling techniques and developed by William L. Jorgensen at the Yale University Department of Chemistry .

The other popular force fields like AMBER, CHARMM, and GROMOS have been developed mainly for molecular dynamics of macromolecules like proteins and also useful for the energy minimizing.