Interaction function and force fields¶
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
- On top of an atom
- As a linear combination of two atoms (
Fig. %s2) - On the line through two atoms, with a fixed distance (
Fig. %s2fd) - As a linear combination of three atoms (
Fig. %s3) - In the plane of three atoms, with a fixed distance (
Fig. %s3fd) - In the plane of three atoms, with a fixed angle and distance (
Fig. %s3fad) - As a non-linear combination of three atoms, out of plane (
Fig. %s3out) - From four atoms, with a fixed distance, see separate
Fig. %s - A linear combination of \(N\) atoms with relative weights \(a_i\)
- Long Range Electrostatics
- Long Range Van der Waals interactions
- Force field