[22] Modeling DNA structures : molecular mechanics and molecular dynamics

There are several tools to improve initial structural estimates of a molecule under study. The methods described in this section weight the structural models according to the approximate internal energy as a function of the atomic coordinates provided by a force field. The method of conjugated gradients is a powerful tool to find the way downhill toward a local minimum. Surmounting barriers and escaping local minima require nonlocal optimization procedures. Of the various possible choices the Bremermann method has been described in greatest detail. The central idea for the implementation of this method is its application to a small number of relevant degrees of freedom, allowing the remaining ones to relax to a local energetic minimum. Monte Carlo methods may be used to obtain statistical averaged quantities. Again the convergence of this method may be considerably increased if the randomly chosen directions mainly concentrate on the relevant directions. Molecular dynamics calculations not only provide averaged quantities but also give information about time-dependent processes