the statement "if trajectory is from constant pressure simulation
actual box size is taken from trajectory" means exactly what it says, namely that if you have a trajectory that was performed using constant pressure (in which case the box size may vary), the box size at each step (which in this case is stored in the trajectory) is taken from the trajectory. you do not have to do anything about it.

Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden