Harmonic bond¶

Description¶

The harm_bond type of bond potential calculates the standard harmonic bond potential given by

\[ E = \frac{1}{2} k \left ( r -r_0 \right )^2 \]

with \(k\) and \(r_0\) the potential parameters decribed in the following table.

Parameter	Units	Description
\(k\)	mass/time\(^2\)	spring constant
\(r_0\)	distance	equilibrium bond length

YAML syntax¶

compute_force_bond:
  potentials_for_bonds:
    - types: [STRING, STRING]
      potential: harm_bond
      parameters:
        r0: VALUE UNITS
        k: VALUE UNITS

STRING = Name of the atom type (specie) involved in the bond.
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_bond:
  potentials_for_bonds:
    - types: [CA, CA]
      potential: harm_bond
      parameters:
        r0: 1.400000e-10 m
        k: 6.521298e+02 J/m^2

Systems with several atom types (species)

compute_force_bond:
  potentials_for_bonds:
    - types: [CA, CA]
      potential: harm_bond
      parameters:
        r0: 1.400000e-10 m
        k: 6.521298e+02 J/m^2
    - types: [CA, CH3]
      potential: harm_bond
      parameters:
        r0: 1.510000e-10 m
        k: 4.407786e+02 J/m^2