19 Computer Modelling and Molecular Dynamics Simulation of Biomolecules
Maria Reif and Martin Zacharias
Physics Department T38, Technical University of Munich, James‐Franck‐Str. 1, 85748 Garching, Germany
19.1 Significance
Computational modelling and simulations have become standard tools in (bio)chemistry. It is important not to use these tools as ‘black box’ approaches but to understand the underlying physical and algorithmic principles. It requires also careful preparation of the simulation or modelling input by the user and careful analysis of the results. Critical analysis is essential because the computational study of a system always relies on a model representation of the real system and thus comes with approximations that may impact the results [1–3]. A user can, however, only critically analyse the results of a computer modelling or simulation procedure if he/she has sufficient knowledge concerning the limitations of the underlying model. The present chapter will provide a basis for understanding the principles of computer modelling and molecular dynamics (MD) simulation of biomolecules. Further reading suggestions are listed at the end of the chapter.
In general, computational modelling and simulation is widely applied in many areas of science, not only (bio)chemistry. It allows studying systems or processes that are elusive to experimental study, e.g. modelling the crash of a car or aeroplane. In (bio)chemistry, the most important advantage of computational ...