CHARMm systems integration

The CHARMM code, version c25bl, was chosen for integration with the metal potential. CHARMM is a multi-purpose molecular dynamics program [35], which uses empirical potential energy functions to simulate a variety of systems, including proteins, nucleic acids, lipids, sugars and water. The availability of periodic boundary conditions of various lattice types (for example cubic and orthorhombic) makes it possible to treat solids as well as liquids. 

Since the brilliant conceptual proposal by Warshel and Levitt [1], the hybrid method of QM/MM has been extensively applied to simulate some very large systems, such as enzymes, nano-scale materials etc. The purpose of this chapter is not to give a complete review of the QM/MM methods, because the developments and applications of QM/MM methods have been well documented and reviewed in many previous articles, for example. Refs. [2-5]. We try to in this manuscript introduce one of recent developed semi-empirical methods, self consistent charge density tight binding (SCC-DFTB) method [6], and its applications to enzymatic processes when integrated with CHARMM force field. 

By integrating the Newtonian Equations of Motion, Molecular Dynamics simulations are able to describe the behavior of particles in a certain system within the observed period of time. The interaction of the atoms is described by the potential energy fxmction of the given force field [e.g. Amber (Cornell et al, 1995), CHARMM (Brooks et al., 1983), GROMOS (Scott et al., 1999), OPLS (Jorgensen Rives, 1988)]. Nowadays, there is an ongoing effort to ameliorate these parameters in a need for models being as less artificial as possible. 

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