Gaussian

The Gaussian potential creates a soft, bell-shaped interaction between particles. It’s useful for modeling polymer bonds or other soft interactions where a harmonic potential might be too stiff.

\[U = -E \exp\left(-\frac{(r-r_0)^2}{2D}\right)\]

where:

\(E\) is the well depth
\(r_0\) is the equilibrium distance
\(D\) is related to the width of the Gaussian

type: Bond2, Gaussian
parameters: None
data:
- id_i: int: Id of one particle
- id_j: int: Id of the other particle
- E : real: Well depth \([energy]\)
- r0 : real: Equilibrium distance \([distance]\)
- D : real: Width parameter \([distance]^2\)

Example:

"gaussianBonds":{
  "type":["Bond2","Gaussian"],
  "parameters":{},
  "labels":["id_i", "id_j", "E", "r0", "D"],
  "data":[[0, 1, 1.0, 1.0, 0.1],
          [1, 2, 1.0, 1.1, 0.1],
          [2, 3, 1.0, 0.9, 0.1]]
}

GaussianCommon_E_r0_D

Gaussian bonds variant with common parameters (E, r0, and D) for all bonds.

type: Bond2, GaussianCommon_E_r0_D
parameters:
- E : real: Common well depth for all bonds \([energy]\)
- r0: real: Common equilibrium distance for all bonds \([distance]\)
- D : real: Common width parameter for all bonds \([distance]^2\)
data:
- id_i: int: Id of one particle
- id_j: int: Id of the other particle

Example:

"gaussianBondsCommon":{
  "type":["Bond2","GaussianCommon_E_r0_D"],
  "parameters":{"E":1.0,
                "r0":1.0,
                "D":0.1},
  "labels":["id_i", "id_j"],
  "data":[[0, 1],
          [1, 2],
          [2, 3]]
}