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Bonds

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


\begin{displaymath}
U_{harm}(r) = k(r - r_0)^2
\end{displaymath} (4)

and Morse potential:


\begin{displaymath}
U_{morse}(r) = D\big(1-\exp(-\rho(r-r_0))\big)^2
\end{displaymath} (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:


next up previous contents
Next: Covalent angles Up: Description of the molecular Previous: Molecular geometry and non-bonded   Contents
Alexander Lyubartsev 2015-02-06