Shortest bond length¶

The shortest bond length CV is similar to the normal bond length, but is chosen as the minimum of a set of bonds between atom $i$ and a list of atoms with indices $j, k, l,...$

$d_{\mathrm{min}} = \mathrm{min}\left( \left| r_{j,k,l,...}-r_{i} \right| \right).$

The use of the shortest bond length is invoked by the following block in the meta-config.json file. atoms1 is the fixed atom $i$ and atom2 is a list of additional atom indices $j,k,l,...$ to be compared:

"collective variables": [
  {
    "type": "shortestbond",
    "name": "shortest bond length between atom i and a set of other atoms",
    "atom1": i,
    "atom2": [j, k, l, ...]
  },
  ...
]