BestChenHummerAngular

The BestChenHummerAngular potential is a specialized angular potential developed by Best, Chen, and Hummer for protein modeling [BestChenHummer]. It combines two Gaussian-like terms to create a potential with two minima.

\[U = -\frac{1}{\gamma} \ln \left( e^{-\gamma(k_\alpha(\theta-\theta_\alpha)^2 + \epsilon_\alpha)} + e^{-\gamma k_\beta(\theta-\theta_\beta)^2} \right)\]

where:

  • \(\gamma\), \(k_\alpha\), \(k_\beta\), \(\theta_\alpha\), \(\theta_\beta\), and \(\epsilon_\alpha\) are constants defined in the potential

  • \(\theta\) is the current angle between the three particles

  • type: Bond3, BestChenHummerAngular

  • parameters: None

  • data:

    • id_i: int: Id of the first particle

    • id_j: int: Id of the central particle

    • id_k: int: Id of the third particle

Example:

"bestChenHummerAngularBonds":{
  "type":["Bond3","BestChenHummerAngular"],
  "parameters":{},
  "labels":["id_i", "id_j", "id_k"],
  "data":[[0, 1, 2],
          [1, 2, 3],
          [2, 3, 4]]
}

Warning

The potential parameters are hardcoded in the potential implementation (taken from [BestChenHummer]). The potential is only defined for KcalMol_A units, if other units are selected an error will be raised.

[BestChenHummer] (1,2)

Best, Robert B., Yng-Gwei Chen, and Gerhard Hummer. “Slow protein conformational dynamics from multiple experimental structures: the helix/sheet transition of arc repressor.” Structure 13, no. 12 (2005): 1755-1763.