Bond2

Possibly the most common bonds within this category are those involving two particles. These types of interactions are frequently used in modeling systems:

topology:
  forceField:
    # ...
    bond2_example1:
      type: ["Bond2", "Harmonic"]
      labels: ["id_i", "id_j", "K", "r0"]
      data:
        - [5, 6, 2.1, 0.2]
        - [6, 7, 2.6, 1.2]
        - [7, 8, 3.2, 3.8]
    bond2_example2:
      type: ["Bond2", "FeneCommon_K_R0"]
      parameters:
        K: 3.2
        R0: 4.0
      labels: ["id_i", "id_j", "r0"]
      data:
        - [8, 9, 11.3]
        - [9, 10, 1.5]
        - [10, 11, 2.8]
    # ...

The example demonstrates the application of both a harmonic potential and a FENE potential. In the latter case, the “FeneCommon_K_R0” version uses shared parameters K and \(R_0\) for all bonds, specified in the “parameters” field. Such variations of potentials are common in UAMMD-structured, aiming to simplify the input.

To name a few, Morse potentials are available, as well as Lennard-Jones potentials used in coarse-grained models for proteins. This context also includes potentials for mimicking the effects of hydrophobic interactions. Moreover, there are versions of the harmonic potential modified with the \(\lambda\) parameter, enabling their use in Thermodynamic Integration.

Available Bond2 potentials: