Two types of bonds are implemented, standard harmonic bond (Note: no factor 1/2 in the potential):

and Morse potential:

Harmonic bonds may be also used for description of the so-called Urey-Bradley term which is a harmonic potential between the 1-3 neighbors (atoms separated by two covalent bonds). This term is included for example into CHARMM force field as a part of interaction potential for covalent angles.

The first line of the bond section of a `.mmol`

file is the number
of bonds. Then lines, one per each bond, follow with parameters for each bond.
Each line consists of the following fields:

- The first is the type of the bond potential. Available values are 0
(harmonic bond), 1 (Morse potential) and 2 (Urey-Bradley term). In the case
of the Urey-Bradley term, the interaction is calculated exactly as in the
case of a harmonic bond (type 0), but the corresponding bond is not accounted
for definition of 1-3 and 1-4 neighbors. It is also not accounted for in
constraint dynamics (that is, constraints are not applied for these bonds)
- The second and third parameters are atom numbers which are linked by the bond.
- The fourth field is the equilibrium bond length in Å. It may be
set negative, in such a case the equilibrium bond length will be taken
from the corresponding coordinates in the fisrt section of the
`.mmol`

file. - The 5-th parameter is the force constant
in
- The 6-th and 7-th parameters are used only for the Morse-type bonds and define the () and () parameters of the Morse potential respectively