Update to include revisions made for AR; minor other adjustments

[davidlmobley]

This update:

• [x] Updates README.md to reflect #26
• [x] Makes various minor changes requested by Annual Reviews, such as an additional discussion of why lysozyme was chosen, and making the scope of the paper more clear in the abstract and intro. An explanation of SAMPL and D3R is also included in a new subsection
• [x] Fixes an issue with a reference
• [x] Lists my new affiliation
• [x] Increments version number in paper
• [x] Updates README.md to indicate these changes
• [x] Updates text to reflect available of inputs for host-guest systems in repo (closing #22)