[docs] we should point out some example(s) on how to read out the trajectories from our output files  #916

@RiesBen
I checked again. State A is Valine and State B is Alanine. So, the ddg should be positive.

Also, I am wondering why the intermediates are needed in OpenFE if they are not used in perses and FEP+. I think FEP+ uses restraints on the backbone of the protein/peptide which may help with convergence. Is there a way to do the same with openFE to test if this is the source of convergence problems?

I think it would also be useful to visualize the trajectories. Are there any scripts available to extract trajectories from the saved simulation.nc file?

Originally posted by @amin-sagar in #889 (reply in thread)