Amber solvatebox: How do I remove water that has traveled away I used Amber's solvatebox function with a small polypeptide and tip3p water with a distance of 15 angstroms between the molecule and the edge of the box.

After I ran dynamics, I tried to view the output by removing water from view in Jmol, but I had a really hard time rotating the polypeptide. When I viewed it with water, I found that the difficulty in rotating was because the radius of rotation (are those the right words?) was extremely large because some waters floated off in the distance.



I want to remove these stray waters. How would I go about doing that? Would I just crack open the output and remove those waters by deleting lines that contain information for those particular waters?
This has nothing to do with box walls (there are no walls!) or restraining the waters. You do not want to do that!

Do not confuse periodic boundary conditions with wrapping to the central cell. Look at the amber tutorials, it is all explained there.

You either need to set iwrap=1 in your amber minor put your trajectory trough cpptraj and use autoimage. 

Again, all in the tutorial and manuals.