Bond length¶

The bond length between two atoms is one of the easiest CVs to be used in a metadynamics simulation. It is simply defined by the length of the vector between to atoms $i$ and $j$

$d_{ij} = \left| r_{j}-r_{i} \right|.$

The use of the bond length is invoked by the following block in the meta-config.json file:

"collective variables": [
  {
    "type": "bond",
    "name": "bond length between two atoms",
    "atoms": [i, j]
  },
  ...
]

Apart from type and name, only the indices of the contributing "atoms" are needed.