Manual fixes

Manual fixes

* updates for cut-off schemes
* used more Roman fonts for abbreviations that are not algebraic
* fixed layout and bounding boxes of figures
* removed references to removed GROMACS-87 force fields
* changed formatting of column of [moleculetype] parameter-listing
  table because we now have some interactions with really long names
  (and some consequent changes to how footnotes and labels
  have to work)
* removed out-of-date appendix B section on Modifying GROMACS
* fixed aspects of CHARMM description, including adding the second
  reference for nucleic acids, and adding a link to the CHARMM36 port

Change-Id: Icb8c0a6087af282a653bb528d71f77e1bb04fae1