Molecular_potential_energy

Computation of the potential energy of a molecule Reference Manual – User Manual . Authors: F. Cazals and A. Chevallier and T. Dreyfus

Main classes:

• T_Phi_psi_dihedral_angles_visitor :
  Defines iterator over all successive pairs of dihedrals.

• T_Unbonded_particles_visitor :
  Defines iterator over all distinct pairs of particles.

• T_Unbonded_particles_with_threshold_visitor :
  Defines iterator over all distinct pairs of particles.

• T_Bonded_particles_visitor :

Defines iterator over the bonds of a covalent structure.

• T_Bond_angles_visitor :

Defines iterator over the bond angles of a covalent structure.

• T_Dihedral_angles_visitor :

Defines iterator over the dihedral angles of a covalent structure.

• T_Improper_angles_visitor :

Defines iterator over the improper angles of a covalent structure.

• T_Molecular_potential_energy_bond_length_term_harmonic :

Defines the standard term associated to the bond length contribution.

• T_Molecular_potential_energy_bond_angle_term_harmonic :

Defines the standard term associated to the bond angle contribution.

• T_Molecular_potential_energy_bond_angle_term_Urey_Bradley :

Defines the Urey-Bradley term associated to a bond angle.

• T_Molecular_potential_energy_torsion_angle_term_harmonic :

Defines the harmonic term associated to the proper dihedral angle contribution.

• T_Molecular_potential_energy_torsion_angle_term_periodic :

Defines the periodic term associated to the proper dihedral angle contribution.

• T_Molecular_potential_energy_torsion_angle_term_Fourier :

Defines the Fourier term associated to the proper dihedral angle contribution.

• T_Molecular_potential_energy_torsion_angle_term_Ryckaert_Bellemans :

Defines the Ryckaert_Bellemans term associated to the proper dihedral angle contribution.

• T_Molecular_potential_energy_cmap_term :

Defines the CMap term associated to a pair of proper dihedral angles.

• T_Molecular_potential_energy_Lennard_Jones_term :

Defines the standard term associated to the Lennard Jones contribution.

• T_Molecular_potential_energy_electrostatic_term :

Defines a standard term associated to the electrostatic contribution.

• T_Molecular_potential_energy_contribution :

Contribution of an energy term to the potential energy function.

• T_Molecular_potential_energy_bonded_contribution :

Contribution of all bonded energy terms to the potential energy function.

• T_Molecular_potential_energy :

Potential energy function adding up all the input contributions (C++11 only).

• T_Molecular_covalent_structure_bond_length_gradient : Defines the gradient associated to the bond length.

• T_Molecular_covalent_structure_bond_angle_gradient :

Defines the gradient associated to the bond angle.

• T_Molecular_covalent_structure_torsion_angle_gradient :

Defines the gradient associated to the torsion angle.

• T_Molecular_potential_energy_bond_length_gradient_harmonic :

Defines the standard gradient associated to the bond length contribution.

• T_Molecular_potential_energy_bond_angle_gradient_harmonic :

Defines the standard gradient associated to the bond angle contribution.

• T_Molecular_potential_energy_bond_angle_gradient_Urey_Bradley :

Defines the Urey-Bradley gradient associated to a bond angle.

• T_Molecular_potential_energy_torsion_angle_gradient_harmonic :

Defines the harmonic gradient associated to the proper dihedral angle contribution.

• T_Molecular_potential_energy_torsion_angle_gradient_periodic :

Defines the periodic gradient associated to the proper dihedral angle contribution.

• T_Molecular_potential_energy_torsion_angle_gradient_Fourier :

Defines the Fourier gradient associated to the proper dihedral angle contribution.

• T_Molecular_potential_energy_torsion_angle_gradient_Ryckaert_Bellemans :

Defines the Ryckaert_Bellemans gradient associated to the proper dihedral angle contribution.

• T_Molecular_potential_energy_torsion_angle_gradient_in_linear_structure :

Defines the gradient associated to the torsion angle contribution in a linear structure.

• T_Molecular_potential_energy_Lennard_Jones_gradient :

Defines the standard gradient associated to the Lennard Jones contribution.

• T_Molecular_potential_energy_electrostatic_gradient :

Defines a standard gradient associated to the electrostatic contribution.

• T_Molecular_potential_energy_gradient_contribution :

Contribution of an energy gradient term to the potential energy gradient function.

• T_Molecular_potential_energy_gradient :

Sum of the contributions of an energy gradient term to the potential energy gradient function.

• T_Molecular_potential_energy_numerical_gradient :

Computes numerically the gradient of a potential energy function.

• T_Molecular_potential_energy_torsion_angle_in_linear_structure_term :

Defines the term associated to the torsion angle contribution in a linear structure.