Canonical unit conversions for force field parameters.
ForceField stores all parameters in a canonical unit system:
============ ========================
Parameter Canonical unit
============ ========================
bond_k kcal/(mol·Å²)
bond_eq Å
angle_k kcal/(mol·rad²)
angle_eq degrees
torsion_k kcal/mol
vdw_radius Å
vdw_epsilon kcal/mol
============ ========================
Energy convention: E = k·(x − x₀)² (no ½ factor), matching AMBER.
Loaders convert from format-native units to canonical on load.
Savers convert from canonical back to format-native on save.
Engines convert from canonical to engine-native at the boundary.
mm3_bond_k_to_canonical(k: float) -> float
Convert MM3 bond force constant (mdyn/Å) to canonical (kcal/mol/Ų).
Source code in q2mm/models/units.py
| def mm3_bond_k_to_canonical(k: float) -> float:
"""Convert MM3 bond force constant (mdyn/Å) to canonical (kcal/mol/Ų)."""
return k * MDYNA_TO_KCALMOLA2
|
canonical_to_mm3_bond_k(k: float) -> float
Convert canonical bond force constant (kcal/mol/Ų) to MM3 (mdyn/Å).
Source code in q2mm/models/units.py
| def canonical_to_mm3_bond_k(k: float) -> float:
"""Convert canonical bond force constant (kcal/mol/Ų) to MM3 (mdyn/Å)."""
return k * KCALMOLA2_TO_MDYNA
|
mm3_angle_k_to_canonical(k: float) -> float
Convert MM3 angle force constant (mdyn·Å/rad²) to canonical (kcal/mol/rad²).
Source code in q2mm/models/units.py
| def mm3_angle_k_to_canonical(k: float) -> float:
"""Convert MM3 angle force constant (mdyn·Å/rad²) to canonical (kcal/mol/rad²)."""
return k * MDYNA_RAD2_TO_KCALMOLRAD2
|
canonical_to_mm3_angle_k(k: float) -> float
Convert canonical angle force constant (kcal/mol/rad²) to MM3 (mdyn·Å/rad²).
Source code in q2mm/models/units.py
| def canonical_to_mm3_angle_k(k: float) -> float:
"""Convert canonical angle force constant (kcal/mol/rad²) to MM3 (mdyn·Å/rad²)."""
return k * KCALMOLRAD2_TO_MDYNA_RAD2
|