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?