Interactions inputΒΆ

Interactions describe the energies between atoms - or more general - between interaction sites. These energies arise due to covalent bonding of atoms to form molecules, short-range van der Waals or long-range Coulombic energies. To describe interactions we use potentials which are functions that take a set of parameters and geometrical coordinates (for example distances or angles) as input and yield energies and forces. A set of potential functions and parameters to describe energies and forces of a molecule is also often called force field. We will use the terms interactions and force field interchangeably.

To be more specific, we distinguish between the following contributions:

  • pairs are van der Waals interactions between pairs of atoms;
  • bonds describe the energy between bonded atoms;
  • angles and dihedrals describe energy contributions due to bending and twisting of bonded atoms;
  • coulomb and charges describe long-range contributions due to electrostatic interactions;
  • the global section describes additional parameter that apply to all the energy contributions.

Information about interactions for pairs, bonds, angles and dihedrals are organized as TOML tables. The coulomb section contains information about the treatment of long-range electrostatic interactions and the charges section defines the partial charges of the atoms.