GROMACS version: 2021.4
GROMACS modification: No
Here post your question
I randomly put small molecules in a water box with protein. I don’t know how to handle cyclicality right now. After I treated the trajectories with -pbc mol and -pbc nojump, the proteins remained intact, but the small molecules remained outside the water box. So how do I deal with periodicity in this case so that the trajectories of both the protein and the small molecule remain intact?