Skip to content

OPLS bond

Description

The opls_bond type of bond potential calculates the type of bond usual in the OPLS force field:

\[ E = k \left ( r -r_0 \right )^2 \]

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: opls_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: opls_bond
      parameters:
        r0: 1.400000e-10 m
        k: 326.0649 J/m^2

Systems with several atom types (species)

compute_force_bond:
  potentials_for_bonds:
    - types: [CA, CA]
      potential: opls_bond
      parameters:
        r0: 1.400000e-10 m
        k: 326.0649 J/m^2
    - types: [CA, CH3]
      potential: opls_bond
      parameters:
        r0: 1.510000e-10 m
        k: 220.3893 J/m^2