Outdated description of modeller.addSolvent

[schuhmc]

This is similar to openmm/openmm#5059

In the protein in water tutorial example, it states the following:

openmm-cookbook/notebooks/tutorials/protein_in_water.ipynb

Line 166 in 2158655

"This command creates a box that has edges at least 1nm away from the solute and fills it with water molecules. Addionally it adds in the required number of CL and Na ions to make the system charge neutral."

If I understand it correctly, the padding is not the minimum distance to the box edge, but to the next replica. The minimum distance to the box edge is therefore half the padding.

I have not checked any other examples in this repository, but that would probably be a good thing to do in order to prevent misunderstandings.