Bonds

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

$$U_{harm}(r) = k(r - r_0)^2$$ (4)

and Morse potential:

$$U_{morse}(r) = D\big(1-\exp(-\rho(r-r_0))\big)^2$$ (5)

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 $r_0$ 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 $k$ in $kJ/mol/\AA^2$

• The 6-th and 7-th parameters are used only for the Morse-type bonds and define the $D$ ($kJ/mol$) and $\rho$ ($\AA^{-1}$) parameters of the Morse potential respectively