Molecular Mechanics

You've selected a Cyclohexane moleculear mechanics simulation.

For the simulation to run, you MUST activate both of these buttons.

The potential energy of the cyclohexane molecule will be minimized numerically with respect to the positions of all its constituent atoms. Three algorithms are available for this purpose:

Steepest Descents - used if the gradients in energy are large.
Conjugate Gradients - used if the gradients in energy are intermediate.
Newton's method -used if the gradients in energy are low.

You may select the total number of iterations you wish to allow, and the numerical methods will be chosen automatically based on the magnitudes of the energy gradients. The more iterations you choose, the longer the simulation runs, and the better chance it has to reach the true minimum energy configuration of the molecule.

Iteration Limit

It is also wise to limit the bounds of displacement of each atom during any single iteration. This helps to avoid pathological instabilities associated with some of the numerical minimization algorithms. A larger limit allows for faster convergence to a minimum energy, but at greater risk of instability.

Movement Limit

Numerical minimization algorithms require some criterion for when to stop iterating. The limit on maximum number of iterations is one such criterion, but it does not ensure any properties about the optimality of the energy of the molecule. Here you may select a convergence criterion based on energy: when the change in energy of the molecule during one iteration is less than the specified convergence, the algorithm assumes that the optimum has been found.

final convergence