AMBER Archive (2008)
Subject: AMBER: solvateBox/solvateDontClip
I would like to know what is actually a difference between the commands: 'solvateBox', and 'SolvateDontClip'. I have read about this in the Amber Users' Manual, of course; I know that 'solvateDontClip' makes bigger boxes (more solvent included), but I do not know what is the difference between 'total bounding box for atom centers' and 'total vdw box size'. What does 'hot-spots' mean, with reference to solvent? The best answer for me could be a picture. Thank you in advance.
Best regards in New Year !