New and reorganized documentation

Re-organized a lot of existing content and deployed it with Sphinx. Install guide, user guide, reference manual, developer manual, Doxygen source-code documentation, and overall webpage now all builds automatically from the source code, so that there is complete documentation that matches the version.

This will permit us to have much more cross-referencing, which should help everyone understand how things work.

Imported some documentation from the wiki to the new user guide. More to follow - contributions welcome!

Tools documentation (man gmx-tool and web pages) now also generated with Sphinx.

Documented the use of alternating electric fields.

Removed some defunct sections from the reference manual.

Made it easier to find the selection help.

Replaced gromacs.7 man page with gmx.1

issue 1242

Corrected force-switch manual section

There was a factor alpha missing in the formulas for parameter A and B for the force switch function (the code was correct). Also removed the introduction and formulas for switching the Coulomb function, since that’s a bad thing to do.

Added new documentation for curve fitting in GROMACS analyis stools

Manual section 8.6 documents old and new behaviour for curve fitting, particularly as used in auto-correlation analysis.

Reinstated documentation for membrane embedding

These were killed by mistake when the once-separate g_membed program was merged into mdrun.

issue 1724.

Fixed documentation of function types of dihedrals

The function-type indices for restricted dihedrals and combined bending-torsion interactions were documented the wrong way around.

issue 1796

Updated user guide .mdp example

Updated the mdp file in user guide. Removed obsolete parameters, and chose parameters that will not give error and warning by default. Also removed the contents of mdout.mdp, since the user can easily retrieve that with the given command, and the file is now much larger. Added note on parameters being dependent on force fields. issue 1774.

Added documentation that energygrps don’t work with GPUs