Merge branch 'release-4-5-patches' into release-4-6

Change-Id: Ica87798f46095cf2eaeeeb34314a11c221215c63
Added instructions for using groups in tools

Change-Id: Ic7aa922bc588eaa45a71bfa781b1b3718b747d97
Updated manual note about Fortran

Change-Id: I4a47244a88f6ae155b0d47a52e5ece6cc67719bf
Remove useless blank pages at end of manual

Change-Id: If7f6b0df8e425703646d48ed1e9f5ca3a4bee538
Improved coarse-grained force-field section

Change-Id: Ia1a5f52364159a8c230edcb7e037b7ab5efd76c7
Merge "Updated manual note about Fortran" into release-4-5-patches
Keep CMake quiet about a Cygwin issue

The CMake warning that is suppressed by this does not affect GROMACS
builds.

Change-Id: Ic6c6d73aabc4d1d99eda34d53cfd2ac156d3ce98
Consolidated documentation of .mdp restraint options

Change-Id: I5aa6c5f166405bd0e3afddadac8d2a1d91548cd5
Merge "Keep CMake quiet about a Cygwin issue" into release-4-5-patches
Merge "Consolidated documentation of .mdp restraint options" into release-4-5-patches
Lots of manual updates

In particular, more extensive and effective indexing

Change-Id: I7a40d47c72e9670dfc2de1435b43e94a84b9d5d4
Corrected fourierspacing description

Change-Id: I9ea32d326b83a6af99a324020c36a0d272c9464c
Updated documentation of .rtp [bondedtypes]

Change-Id: I2a0e2ec569c381ea9e0655a704f6d5ed51727304
Changes for free energy and expanded ensemble.

Change-Id: If7b950d1e670cddd4b63f922f8f55c82437e6d81
Small modification to wording regarding negative sigma. Committing this
to the release-4-5-patches branch to be incorporated in 4.6 and master.

Fixes #940.

Change-Id: Ibbf24c25f82babe1d10e1f9b913a5c3d7f25c721
update for improvement to simple SD integrator

Change-Id: If4b3d196e8018c1a768a9035cd6f7b115c63335f
Revert "Updated documentation of .rtp [bondedtypes]"

This reverts commit e7640cfd1cd91dfe7d640cc634a5ef2a9915f147, which was committed before discussion on Gerrit completed
Merge branch 'release-4-5-patches' into release-4-6

Conflicts:
	algorithms.tex
	special.tex

Change-Id: Ia93e9b4db89340298b93bcef31fdde937f2eb916
changed the PPPM section to P3M-AD

Change-Id: Ifc7b893142c0c9a55d80689758aa1aeef76be722
Added description of the new Verlet cut-off scheme

Change-Id: Id980131c678c7902035fdec96dd7b0f3217a5e19