Quartic bond¶

Description¶

The quar_bond type of bond potential calculates a quartic bond potential given by

\[ E = k_2 \left ( r -r_0 \right )^2 + k_3 \left ( r -r_0 \right )^3 + k_4 \left ( r -r_0 \right )^4 \]

with \(k_2\), \(k_3\), \(k_4\) and \(r_0\) the potential parameters decribed in the following table.

Parameter	Units	Description
\(k_2\)	energy/distance\(^2\)	force constant
\(k_3\)	energy/distance\(^3\)	force constant
\(k_4\)	energy/distance\(^4\)	force constant
\(r_0\)	distance	equilibrium bond length

YAML syntax¶

compute_force_bond:
  potentials_for_bonds:
    - types: [STRING, STRING]
      potential: quar_bond
      parameters:
        r0: VALUE UNITS
        k2: VALUE UNITS
        k3: VALUE UNITS
        k4: 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: quar_bond
      parameters:
        r0: 1.400000e-10 m
        k2: 326.0649 J/m^2
        k3: 0.0 J/m^3
        k4: 0.0 J/m^4

Systems with several atom types (species)

compute_force_bond:
  potentials_for_bonds:
    - types: [CA, CA]
      potential: quar_bond
      parameters:
        r0: 1.400000e-10 m
        k2: 326.0649 J/m^2
        k3: 0.0 J/m^3
        k4: 0.0 J/m^4
    - types: [CA, CH3]
      potential: quar_bond
      parameters:
        r0: 1.510000e-10 m
        k2: 220.3893 J/m^2
        k3: 0.0 J/m^3
        k4: 0.0 J/m^4