Bonds

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

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

and Morse potential:

  $\displaystyle
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: