i think it was this post: Removing pbc effect - #12 by alevilla
in particular one of the answers which suggested nojump and the center. The -fit rot+trans was one i found somewhere else.
The suggested workflow you posted i tried before, with a similiar result to my first try. I think the problem is with the nojump command. Currently I’m making another trajectory because i think i used the center command when i was removing the solvent from the trajectory which could be the reason why nojump made problems. And thank you for your help.