DihedralsMeasure

The DihedralsMeasure step calculates and records the dihedral angles for specified sets of four particles over time.

Output format:

# Step 1
dihedral1 dihedral2 dihedral3 ...
# Step 2
dihedral1 dihedral2 dihedral3 ...
# Step 3
dihedral1 dihedral2 dihedral3 ...
...

---

• type: ParticlesListMeasure, DihedralsMeasure

• parameters:

  • outputFilePath: string: Path to the output file

• data:

  • id_i: int: ID of the first particle in the dihedral

  • id_j: int: ID of the second particle in the dihedral

  • id_k: int: ID of the third particle in the dihedral

  • id_l: int: ID of the fourth particle in the dihedral

Example:

"dihedralsMeasure":{
  "type":["ParticlesListMeasure","DihedralsMeasure"],
  "parameters":{
    "intervalStep": 10000,
    "outputFilePath": "dihedrals.dat"
  },
  "labels":["id_i", "id_j", "id_k", "id_l"],
  "data":[
    [1, 2, 3, 4],
    [2, 3, 4, 5],
    [3, 4, 5, 6]
  ]
}

Note

The output file will contain the step number and the dihedral angle for each specified set of four particles.

Tip

This measure is particularly useful for analyzing the conformational changes of molecules, such as protein backbone dihedrals or torsion angles in polymers.