Abstract
This section provides a compact description of the basics of MD simulation. It only covers topics that are required to understand MD simulation in process engineering, i.e. in particular molecular modeling, the computation of potentials and forces, as well as the efficient identification of neighboring molecules. Here focus is put on single- and multi-center interactions based on the Lennard-Jones potential for short-range interactions. These detailed descriptions help to elaborate the differences between MD in process engineering and other fields and motivate the development of a specialized code. Such a code is ls1 mardyn, whose optimizations are discussed in the up-coming chapters. At the end of the section we provide the general layout of the software.
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Heinecke, A., Eckhardt, W., Horsch, M., Bungartz, HJ. (2015). Molecular Dynamics Simulation. In: Supercomputing for Molecular Dynamics Simulations. SpringerBriefs in Computer Science. Springer, Cham. https://doi.org/10.1007/978-3-319-17148-7_2
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