So far, we have discussed the functional form of the energy terms and the parameters used to define these potentials in a molecular mechanics program. Clearly, these are primarily responsible for the accuracy of the computed structures, strain energies and molecular vibrations. However, they are not the only factors that have an influence on the calculation and the result. The type of input accepted by the program, the output produced, and the algorithms used to achieve energy minimization can impact on the accuracy of the results, limit the type of problems that can be handled, and the type of constraints that can be imposed. It is, therefore, important to understand the advantages and disadvantages of different methods for carrying out energy minimization.
4.1 Input and Output
The type of input and output data that are available, and the way in which they are handled, not only has a strong impact on the aesthetics and ease of use of a molecular modeling package, but also affects the accuracy of the interpretation of the results and the insights obtained. Ideally, molecular mechanics routines should be combined with molecular graphics packages that allow the importation of experimental structural data, the building of new molecules and the representation of these molecules. The manipulation of the calculated geometries in three-dimensional space should occur in real time. There are many such programs available, but molecular graphics is beyond the scope of this book. The molecular mechanics programs listed in Appendix 3 are either available as packages with a graphical interface or they are easily adapted to other graphics packages.
Potential energy surfaces usually have many different minima. The starting structure, the algorithm used for strain energy minimization and the concurrent geometry optimization have a strong influence on the particular minimum to which the refinement converges, and also on the time required for the optimization. The type of minimum, whether it is a global or local minimum, can be of importance Molecular Modeling of Inorganic Compounds. Third Edition.