Hi everyone,

I am running a 10 ns NPT production run MD simulation of a protein-ligand complex. From the finish results, I find my ligand leaves the original binding pocket (left figure), even leaving the water box. Then, I use Recenter Solvated System Trajectory protocol to process the same solvated protein-ligand trajectory, I find my ligand still in the original binding pocket(right figure), and the ligand not leaving the water box. So, I am confused, which result is true?

Thanks