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Key concepts from statistical mechanics are particularly important and prevalent in molecular simulations:
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\begin{itemize}
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\item Ensembles, distribution functions for different ensembles. Equivalence of ensembles
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\item What equilibrium means and the difference between equilibrium and non-equilibrium.
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For instance, what is usually called an ``equilibrium trajectory'' generally will not embody a good sample of the equilibrium ensemble due to insufficient sampling.
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On the other hand, truly non-equilibrium conditions such as driven transitions and relaxation are fundamentally different.
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Note that relaxation can occur to the equilibrium ensemble or a non-equilibrium condition (e.g., steady state).
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\item Clarify differences between nonequilibrium ensembles: driven
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nonequilibrium steady-state, systems driven out of equilibrium by a time-dependent field, systems initially out of equilibrium but relaxing
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to equilibrium
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\item Time averages and ensemble averages
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\item Fluctuations
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\item Correlation functions
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\item Definitions of various ensembles
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\item Time averages and ensemble averages
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\item Equilibrium versus non-equilibrium
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\end{itemize}
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\todo[inline, color={yellow!20}]{DLM: This list is bothering me because it is longer than the others, has more statements in it, and doesn't totally connect with what's in this section. Not sure what to do with it.}
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\todo[inline, color={yellow!20}]{DLM: This list is bothering me because it is longer than the others, has more statements in it, and doesn't totally connect with what's in this section. Not sure what to do with it. JIM: I've proposed changes. Helpful or not?}
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Traditional discussions of classical statistical mechanics, especially concise ones, tend to focus first or primarily on macroscopic thermodynamics and microscopic \emph{equilibrium} behavior based on the Boltzmann factor, which tells us that configurations $\conf$ occur with (relative) probability $\exp[-U(\conf)/k_B T]$, based on potential energy function $U$ and temperature $T$ in Kelvin units.
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Dynamical phenomena and their connection to equilibrium tend to be treated later in discussion, if at all.
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