Car-Parrinello molecular dynamics simulations and biological systems

The basic concepts of Car-Parrinello molecular dynamics (CPMD) and its application to biological systems are reviewed. In Car-Parrinello simulations the electronic structure is calculated on the fly, i.e., during the course of simulations the potential is adjusted according to the chemical events occurring in the system. This allows for more unbiased simulations of chemical processes, as opposed to classical molecular dynamics, which utilize predefined potentials. In contrast to Born-Oppenheimer molecular dynamics, where the nuclei are propagated under classical equations of motions and where the wave function is calculated in every time step, CPMD maps this two-component classical/quantum system onto a two-component purely classical system. A short introduction into classical mechanics, which provides the equations of motions, is given. DFT will be briefly outlined because it represents the standard method for obtaining the electronic structure during a CPMD simulation. QM/MM approaches, which combine the CPMD method for a core region with a classical description of its environment, are also reviewed. These schemes provide a more reliable description of biological systems, whose properties are strongly influenced by their surroundings. A brief overview over the application of Car-Parrinello simulations to biological systems is provided. Finally, a case study to illustrate some of the basic possibilities of this method is discussed.