Boltzmann distribution, from conformational search

Hence, in the light of our both accounts of causality, the molecular dynamics model represents causal processes or chains of events. But is the derivation of a molecule s structure by a molecular dynamics simulation a causal explanation Here the answer is no. The molecular dynamics model alone is not used to explain a causal story elucidating the time evolution of the molecule s conformations. It is used to find the equilibrium conformation situation that comes about a theoretically infinite time interval. The calculation of a molecule s trajectory is only the first step in deriving any observable structural property of this molecule. After a molecular dynamics search we have to screen its trajectory for the energetic minima. We apply the Boltzmann distribution principle to infer the most probable conformation of this molecule.17 It is not a causal principle at work here. This principle is derived from thermodynamics, and hence is statistical. For example, to derive the expression for the Boltzmann distribution, one crucial step is to determine the number of possible realizations there are for each specific distribution of items over a number of energy levels. There is no existing explanation for something like the molecular partition function for a system in thermodynamic equilibrium solely by means of causal processes or causal stories based on considerations on closest possible worlds. 

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