Q: What is a trajectory?
A trajectory is the time-ordered sequence of system configurations which occur as all the coordinates evolve in time following some rules – hopefully rules embodying reasonable physical dynamics, such as Newton’s laws or constant-temperature molecular dynamics.
Q: What is a trajectory ensemble?
It’s a set of independent trajectories that together characterize a particular condition such as equilibrium or a non-equilibrium steady state. That is, the trajectories do not interact in any way, but statistically they describe some condition because of how they have been initiated – and when they are observed relative to their initialization … see below.