Bond angle¶

An angle is defined by three atoms $i,j,k$ by

$\phi = \cos^{-1}{\left( \ \frac{r_{ij} \cdot r_{kj}}{ \left| r_{ij} \right|\left| r_{kj} \right|} \ \right)},$

where $r_{ij}$ is the connection vector between the atoms $i$ and $j$ . It takes values from 0 to 180 degrees.

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

"collective variables": [
  {
    "type": "angle",
    "name": "bond angle phi",
    "atoms": [i, j, k]
  },
  ...
]

The "atoms" keyword is used for the definition of the involved atoms in consecutive order.