Molecular mechanics force field customization

Most existing molecular mechanics studies of inorganic molecules required careful customization of force field parameters. 

There are many different pieces of code available for molecular mechanics, ranging from the simple, such as MM2, to the elaborate, such as Cerius S YBYL, Spartan, and HyperChem. The code chosen for a particular model of catalytic processes depends on two factors (1) the complexity of the system that is to be studied, and (2) the amount of computer expertise available. Complicated structures, such as surfaces and zeolites, generally require specialized software packages for their visualization typically workers use commercial code with perhaps minor modifications. Simpler systems, such as modeling vanadium oxo species, are amenable to study using simpler codes, such as MM2, that are customized to suit the specific needs of the research group. It should be noted that the various available packages employ different force assumptions and some force fields are more suitable to one kind of application than to another (see Chapter 2). 

The most basic approach to carry out MD simulations for larger systems is to use classical force fields. A variety of different force fields for molecular mechanics (MM) simulations has been developed,which are mainly intended to describe the non-reactive dynamics of large systems. In particular in the field of biochemistry force fields play an essential role to study the complex properties of large biomolecules. However, classical force fields require the specification of the connectivity of the atoms. Therefore, they are not able to describe chemical reactions, i.e., the making and breaking of bonds. To describe reactions, they can be combined with quantum mechanical (QM) methods in so-called QM/MM simulations. In recent years also reactive force fields , e.g. ReaxFF, have been introduced, which overcome this limitation. However, these reactive force fields are typically highly adapted to specific systems by analytic terms customized to describe e.g. certain bonding situations, and only a few applications have been reported so far. 

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