Amnah,
I had this same issue. I went into it in the post that genie alluded to. Genie gave a great example of how to do the “pull” function and I tried my best to go into detail with how to do the approach that Justin suggests. In case you missed the link above:
https://gromacs.bioexcel.eu/t/constraining-terminal-basepairs-in-dna/2549