[gmx-users] smd

[Yixin Ai]

Dear everyone，
    i want to use gromacs to perform the steered molecular dynamcs simulation. My system is the protein-ligand complex in the center of the box an i want to pull out of the ligand form the protein ative site.  i have set the pbc in my mdp file.  However,  after simulation, i find that the ligand out of the box and get into the next unit cell. How does this make sense? should i the box larger to keep the liand in the original unit cell?