Harmonic bending¶

Description¶

The harm_bend type of bending potential calculates the standard harmonic bending potential given by

\[ E = \frac{1}{2} k \left ( \theta -\theta_0 \right )^2 \]

with \(k\) and \(\theta_0\) the potential parameters decribed in the following table.

Parameter	Units	Description
\(k\)	energy	force constant
\(\theta_0\)	angle	equilibrium bending angle

YAML syntax¶

compute_force_bend:
  potentials_for_bends:
    - types: [STRING, STRING, STRING]
      potential: harm_bend
      parameters:
        theta0: VALUE UNITS
        k: VALUE UNITS

STRING = Name of the atom type (specie) involved in the bending angle.
VALUE = Physical value of the intended parameter.
UNITS = Units of the provided value that will be passed to the conversion helper for internal units conversion.

Usage examples¶

Systems with a single atom type (specie)

compute_force_bend:
  potentials_for_bends:
    - types: [CA, CA, CA]
      potential: harm_bend
      parameters:
        theta0: 1.200000e+02 degree
        k: 8.759953e-19 J

Systems with several atom types (species)

compute_force_bond:
  potentials_for_bonds:
    - types: [CA, CA, CA]
      potential: harm_bond
      parameters:
        r0: 1.400000e-10 m
        k: 6.521298e+02 J/m^2
    - types: [CA, CA, CR4]
      potential: harm_bond
      parameters:
        theta0: 1.200000e+02 degree
        k: 9.733281e-19 J