Parrinello modeling of biological systems

The exponential increase in computer power and the development of highly efficient algorithms has distinctly expanded the range of structures that can be treated on a first-principle level. Using parallel computers, AIMD simulations of systems with few hundred atoms can be performed nowadays. This range already starts to approach the one relevant in biochemistry. Indeed, some simulations of entire biomolecules in laboratory-realizable conditions (such as crystals or aqueous solutions) have been performed recently [25-28]. For most applications however, the systems are still too large to be treated fully at the AIMD level. By combining AIMD simulations with a classical MD force field in a mixed quantum mechanical/molecular mechanical fashion (Hybrid-AIMD) the effects of the protein environment can be explicitly taken into account and the system size can be extended. 

Even though it is possible to work with fairly sizeable quantum models, an intelligent choice of the crucial part of the system is still the bcisis of any successful modeling. The following different approaches have been applied so far  

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