Force Fields

A force field is a computational method that is used to estimate

the forces between atoms within molecules and also between
molecules.

More precisely, the force field refers to the functional form and
parameter sets used to calculate the potential energy of a
system of atoms or coarse-grained particles in molecular
mechanics, molecular dynamics, or Monte Carlo simulations.
1. Functional Form
 The basic functional form of potential energy in molecular
mechanics includes
1. Bonded terms for interactions of atoms that are linked by
covalent bonds, and
2. Nonbonded (also termed noncovalent) terms that describe the
long-range electrostatic and van der Waals forces.
Etotal = Ebonded + Enon-bonded

Ebonded = Ebond + Eangle + Edihedral

Enon-bonded = Eelectrostatic + Evanderwalls

Molecular mechanics potential energy
function with continuum solvent
1.1 Bond Streching
Ebond = kij / 2 ( lij – l0,ij )
where kij is the force constant, lij is the bond length and l0,ij is the value for
the bond length between atoms i and jwhen all other terms in the force
field are set to 0.
The constant kij determines vibrational frequencies
in molecular dynamics simulations.

1.2 Electrostatic interactions

Ecoulomb = 1/4πε0 qi qj /rij
Electrostatic interactions are represented by a Coulomb energy,
which utilizes atomic charges qi to represent chemical bonding
ranging from covalent to polar covalent and ionic bonding,
where rij is the distance between two atoms i and j.
2. Parameterization
 Force fields define a set of parameters for different types of
atoms, chemical bonds, dihedral angles, out-of-plane
interactions, nonbond interactions, and possible other terms.
 Atom types are defined for different elements as well as for
the same elements in sufficiently different chemical
environments. For example, oxygen atoms in water and an
oxygen atoms in a carbonyl functional group are classified as
different force field types.
 Typical force field parameter sets include values for atomic
mass, atomic charge, as well as equilibrium values of bond
lengths, bond angles, and dihedral angles.
Popular Force Fields
1. Assisted Model Building with Energy
Refinement (AMBER)- It is a family of force
fields for molecular dynamics of biomolecules (widely used
for proteins and DNA) originally developed by Peter
Kollman's group at the University of California, San
Francisco.
2. CHARMM (Chemistry at HARvard Molecular Mechanics) –
originally developed at Harvard, widely used for both small
molecules and macromolecule.
3. MM2- It was developed by Norman Allinger mainly for
conformational analysis of hydrocarbons and other small
organic molecules. It is designed to reproduce the
equilibrium covalent geometry of molecules as precisely as
possible. It implements a large set of parameters that is
continuously refined and updated for many different classes
of organic compounds (MM3 and MM4).