The first three terms above are bonded terms that describe how the energy changes for a particular bond distance, bond angle and dihedral angle. There is one term for each such internal coordinate in the molecule. The parameter, n , is the number of minima or maxima that occur when the torsional angle is rotated through a full 360 o . For instance, in ethane, it has a value of 3. R kl is the distance between them and the A, B, C, and D parameters in these equations are determined from experimental data.
Some force fields use dipole-dipole interactions in place of the simple coulombic terms above.
This more complicated formula is not given above. But to alleviate and accommodate the nonbonded interactions in order to reach a total energy that is minimum, the final geometry will not have these reference values. With these equations, the motions of the molecules can be followed with time by using finite difference methods to integrate the above equations. The system is initialized by randomly assigning velocities to each atom. Thus these equations are applied successively to each particle to generate the full trajectories of all the particles over the entire time span of the simulation.