Problem with protein DNA simulation

GROMACS version:
GROMACS modification: Yes/No
Here post your question I am running a 500ns simulation on a protein DNA crystal structure using AMBER99SB forcefield. However, the DNA seems to get detached from the protein after around 150ns. I tried changing the box dimensions and have rerun the simulation, the same problem persisted. What could be the problem? If this happens, what could the possible explanation for this?
Please let me know.