Reorganize tutorial files and ensure consistency with docs

[sseyler]

The tutorial files that are included in the repository need to be organized for consistency with the documentation (now on RTD). The coord, emin, MD, posres, solvation, and bin directories also do not really need to be there, since the user is expected to generate this directory structure on their own. Also, only the *.mdp files that are referenced in the basic tutorial docs should be included in the repository—some unnecessary ones are lying around.

[sseyler]

To do list:

• Remove coord, emin, MD, posres, solvation, and bin directories
• Update *.mdp files (for newest Gromacs version settings, see what I did with Taylor)
• Ensure consistency between docs and provided files
• Adjust tutorial and included files in light of any changes related to Issue Create separate tutorial for "advanced" AdK Gromacs Tutorial? #4 (advanced AdK tutorial)

[orbeckst]

If you put the TODO list with check mark boxes - [ ] into the initial comment then it will show up with number of checked of items in the issues list.