IDP_Fourier

The IDP_Fourier potential is a specialized dihedral potential designed for modeling Intrinsically Disordered Proteins (IDPs) [Smith2015] .

\[U = \sum_{s=1}^4 [A_s \cos(s\phi) + B_s \sin(s\phi)]\]

where \(A_s\) and \(B_s\) are coefficients determined from simulations of IDPs.

type: Bond4, IDP_Fourier
parameters: None
data:
- id_i: int: Id of the first particle
- id_j: int: Id of the second particle
- id_k: int: Id of the third particle
- id_l: int: Id of the fourth particle

Example:

"idpFourierBonds":{
  "type":["Bond4","IDP_Fourier"],
  "parameters":{},
  "labels":["id_i", "id_j", "id_k", "id_l"],
  "data":[[0, 1, 2, 3],
          [1, 2, 3, 4],
          [2, 3, 4, 5]]
}

Warning

The IDP_Fourier potential uses predefined coefficients and does not require additional parameters per bond [Smith2015]. The IDP_Fourier potential is only available in the KcalMol_A unit system.If other units are used, an error will be raised.

[Smith2015] (1,2)

Smith, W. Wendell, Po-Yi Ho, and Corey S. O’Hern. “Calibrated Langevin-dynamics simulations of intrinsically disordered proteins.” Physical Review E 90, no. 4 (2014): 042709.