A puzzled biologist here! Is molecular dynamics simulations actually run on a single protein molecule to give the structure with minimum Gibbs free energy or does it consider many molecules at once (what I think ensemble is meant to mean)?
Answer
Any given MD simulation acts on only a single instance of the molecule. It simply integrates Newton's second law to produce the trajectory of that molecule over time.
The ensemble refers to the theoretical class of every possible configuration that satisfies some constraint (it's a concept from statistical mechanics). In practice we make the assumption (the ergodic hypothesis) that if you average a quantity over a trajectory for long enough then you will get the same answer as the ensemble average.
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