Question can be general for all systems, but as an illustration, suppose that I have 500ns trajectory of some peptide. Suppose that system converge during last 100ns. Now I want to calculate some property of that peptide. One way is to calculate that property hundred times during last 100ns (timestep 1ns), and then averaged it. But that is tedious.
What alternative methods researchers usually use in that situations?
What I got so far:

Get the average structure (which may not be physical) and calculate property of that structure. Average structure may not be phisical, but will property calculated that way be the same as after averaging described above?

Calculate RMSD or RMSF in reference to average (or some other significant) structure, and take one with minimal deviation

Use gmx cluster somehowâ€¦
I appreaciate your valuable time for any suggestion.