Molecular Dynamics. Observing Matter in Motion
It is particularly important to obtain insights into the structural and dynamical aspects of ordered systems on the atomic level in order to understand the functions of such complex molecular constructions. In many cases, it is impossible to obtain microscopic detail using conventional experimental techniques. However, the genuine explosion of computer resources over the past ten years, together with the development of more effective algorithms, have made it possible to study nanomolecular assemblies of increasing complexity through the methods of theoretical chemistry. The purpose of this chapter is to examine one aspect of theoretical chemistry, namely, statistical simulations of molecular mechanics. The aim of such simulations is to gain access to the atomic detail of condensed matter through computer experiments. There are many techniques available today to do this,including molecular dynamics, stochastic dynamics and its special cases – e.g., Brownian dynamics or Langevin dynamics – or again Monte Carlo simulations. These different theoretical approaches can be viewed in many ways as a bridge between macroscopic experimental observation and its microscopic counterpart. In the following, we shall be mainly concerned with molecular dynamics .
KeywordsMolecular Dynamic Molecular Dynamic Simulation Radial Distribution Function Potential Energy Function Free Energy Calculation
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I would like to thank my colleagues François Dehez, Jérôme Delhommelle, and Mounir Tarek for accepting to check and comment on the text, with suggestions for improving the content.
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