Ab Initio Molecular Dynamics: A Guide to Applications

Ab initio molecular dynamics (AIMD) is an important simulation method applied to understand systems encountered in chemistry and biochemistry, as well as in physics and materials science. It provides means to study complex systems undergoing chemical reactions or phase transitions, as occurring in systems under extreme conditions, or previously unknown compositions. We introduce the basic concepts and methods of AIMD when used together with density functional theory approaches. The connection between the currently most widely used methods, Born–Oppenheimer MD and 2nd Generation Car–Parrinello MD is derived. Important parameters for efficient and accurate simulation protocols are discussed with the focus on the implementations in the CP2K software. Step by step procedures to correctly set up simulations are provided. Sample applications from literature are presented with a special emphasis on the simulation system parameters and protocols used.