Bond4

Bond4 potentials in UAMMD-structured are interactions involving four particles. These are primarily used to model dihedral angles in molecular simulations. A dihedral angle is defined by four particles (i, j, k, l).

The dihedral angle \(\phi\) is the angle between the plane containing particles i, j, k and the plane containing particles j, k, l:

The energy and forces are typically functions of this dihedral angle :math: phi, allowing for the modeling of various molecular conformations and rotational barriers.

topology:
  forceField:
    # ...
    bond4_example:
      type: ["Bond4", "Dihedral"]
      labels: ["id_i", "id_j", "id_k", "id_l", "n", "K", "phi0"]
      data:
        - [16, 17, 18, 19, 1, 43.2, 0.1]
    # ...

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Available dihedral (\(\phi\) dependent) potentials:

• Dihedral
• IDP_Fourier