Bond3

Bond3 potentials in UAMMD-structured are interactions involving three particles. While these can be used for various three-body interactions, they are primarily employed to define angular bonds in molecular simulations. In the context of angular bonds, the three particles (i, j, k) form an angle, with j being the central particle.

The angle \(\theta\) is defined as the angle formed between the vectors j-i and j-k:

The energy and forces are typically functions of this angle θ, \(r_{ji} = r_i - r_j\) and \(r_{jk} = r_j - r_k\), where \(cos \theta = (\vec{r}_{ji} \cdot \vec{r}_{jk}) / (|r_{ji}| |r_{jk}|)\).

Hence, we can define potentials such as \(U(\theta) = 1/2 K(\theta - \theta_0)^2\), which we refer to as “HarmonicAngular” in the following example:

topology:
  forceField:
    # ...
    bond3_example:
      type: ["Bond3", "HarmonicAngular"]
      labels: ["id_i", "id_j", "id_k", "K", "theta0"]
      data:
        - [12, 13, 14, 1.32, 1.15]
        - [13, 14, 15, 3.13, 0.53]
    # ...

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Available angular (\(\theta\) dependent) potentials:

• KratkyPorod
• HarmonicAngular
• BestChenHummerAngular