Statistical mechanics (SM) is a branch of the physical sciences which deals with understanding the statistical behavior of collections of molecules. In the context of molecular simulations, statistical mechanics allows us to compute things like free energies, understand temperature fluctuations, and so on. Rather than repeat text books we refer to some wikipedia pages here.

http://en.wikipedia.org/wiki/Statistical_mechanics - basic background
http://en.wikipedia.org/wiki/Central_limit_theorem - the relation between long time scales in simulation and ensemble averages
http://en.wikipedia.org/wiki/Shannon_sampling_theorem - from this one can derive the maximum time step in a simulation

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Statistical Mechanics

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