KratkyPorod

The Kratky-Porod potential, also known as the worm-like chain model, is used to describe the bending energy of semi-flexible polymers. It penalizes deviations from a straight chain configuration.

\[U = K(1 + \cos\theta)\]

where:

\(K\) is the bending stiffness
\(\theta\) is the angle between two consecutive segments

type: Bond3, KratkyPorod
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
- K: real: Bending stiffness \([energy]\)

Example:

"kratkyPorodBonds":{
  "type":["Bond3","KratkyPorod"],
  "parameters":{},
  "labels":["id_i", "id_j", "id_k", "K"],
  "data":[[0, 1, 2, 10.0],
          [1, 2, 3, 10.0],
          [2, 3, 4, 10.0]]
}

KratkyPorodCommon_K

KratkyPorod bonds variant with a common bending stiffness (K) for all bonds.

type: Bond3, KratkyPorodCommon_K
parameters:
- K: real: Common bending stiffness for all bonds \([energy]\)
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:

"kratkyPorodBondsCommonK":{
  "type":["Bond3","KratkyPorodCommon_K"],
  "parameters":{"K":10.0},
  "labels":["id_i", "id_j", "id_k"],
  "data":[[0, 1, 2],
          [1, 2, 3],
          [2, 3, 4]]
}