Clashed

The Clashed potential is a soft repulsive interaction designed to prevent overlap between particles while allowing for some degree of interpenetration. It is particularly useful in coarse-grained simulations where hard-core repulsions may be too restrictive.

The potential energy is given by:

\[\begin{split}U = \begin{cases} \lambda (d^2 - r^2)^2 & \text{if } r < d \\ 0 & \text{if } r \geq d \end{cases}\end{split}\]

where:

• \(\lambda\) is the strength of the interaction

• \(d = \gamma(r_i + r_j)\) is the interaction distance

• \(r_i, r_j\) are the radii of particles i and j

• \(\gamma\) is a scaling factor for the interaction distance

• \(r\) is the distance between particle centers

---

• type: NonBonded, Clashed

• parameters:

  • lambda: real: Strength of the interaction \([energy]/[distance]^4\)

  • gamma: real: Scaling factor for the interaction distance

• data:

  • name_i: string: Type of particle i

  • name_j: string: Type of particle j

Example:

"clashed":{
  "type":["NonBonded","Clashed"],
  "parameters":{
    "lambda":1.0,
    "gamma":1.1,
    "condition":"all"
  },
  "labels":["name_i", "name_j"],
  "data":[
    ["A", "A"],
    ["A", "B"],
    ["B", "B"]
  ]
}

Note

The Clashed potential uses the radius information stored in the particle data. Ensure that the radii are properly set for each particle before using this potential.

Warning

While the Clashed potential allows for some overlap between particles, it may not be suitable for systems where maintaining strict excluded volume is critical.