Dear all,
If we have a restrained receptor protein in a 10x3x3 water box for steered MD of a ligand, does the distance from the protein to the edges of the box need to be >10Å? I understand that in unrestrained MD, we need to do this so the protein doesn’t see its own periodic image. However, for steered MD, if the receptor remains restrained and distance of the dissociated ligand after MD is far from the pbc image of the receptor, is it ok that it is placed near the edges of the box?