Interaction function and force fieldsΒΆ
To accommodate the potential functions used in some popular force fields (see Interaction function and force fields), GROMACS offers a choice of functions, both for non-bonded interaction and for dihedral interactions. They are described in the appropriate subsections.
The potential functions can be subdivided into three parts
- Non-bonded: Lennard-Jones or Buckingham, and Coulomb or modified Coulomb. The non-bonded interactions are computed on the basis of a neighbor list (a list of non-bonded atoms within a certain radius), in which exclusions are already removed.
- Bonded: covalent bond-stretching, angle-bending, improper dihedrals, and proper dihedrals. These are computed on the basis of fixed lists.
- Restraints: position restraints, angle restraints, distance restraints, orientation restraints and dihedral restraints, all based on fixed lists.
- Applied Forces: externally applied forces, see chapter Special Topics.
- Non-bonded interactions
- Bonded interactions
- Bond stretching
- Morse potential bond stretching
- Cubic bond stretching potential
- FENE bond stretching potential
- Harmonic angle potential
- Cosine based angle potential
- Restricted bending potential
- Urey-Bradley potential
- Bond-Bond cross term
- Bond-Angle cross term
- Quartic angle potential
- Improper dihedrals
- Proper dihedrals
- Tabulated bonded interaction functions
- Restraints
- Polarization
- Free energy interactions
- Methods
- Virtual interaction sites
- Long Range Electrostatics
- Long Range Van der Waals interactions
- Force field