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Biomolecular and Bioanalytical Techniques
book

Biomolecular and Bioanalytical Techniques

by Vasudevan Ramesh
June 2019
Beginner to intermediate content levelBeginner to intermediate
576 pages
25h 29m
English
Wiley
Content preview from Biomolecular and Bioanalytical Techniques

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 [13]. 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 ...

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