Version bumps before release

Change-Id: I5b5ea233c47ce95474dae3b0f71a4ae6ae704f6c
Version bump after 4.6.5 release

Change-Id: I1d1c1ee28d585b6cf4431f9f1ec1a334f68ae6e3
Fix non-critical typo in #ifdef GMX_OMPEN_MP

Added #include to make it work.

Change-Id: Icea244c4fb63aee6ae67a29370d08177a66129a8
Fixed compilation issue due to gcc4.8

by turning off warnings.

Change-Id: Ice3dd8dec8cb9dc590fb293c1face3ed603f7abb
Fixed essential dynamics (ED) continuation from .cpt for reference=average

ED runs where the reference and average structure indices are the same can
crash when continued from checkpoint. For these cases (where reference =
average atom indices) obviously the set of atomic positions for the reference
and average structures is always identical. Therefore, only one of the two
structures is stored (which is the average structure edi->sav). When reading
the old values of these structures from the checkpoint file, edi->sav.x_old
therefore needs to be copied both to xstart and xfit in init_edsam().

Change-Id: Ieb1f029f4a927999dfb4579ee7c3bebe15071dc8
Essential dynamics: move bNeedDoEdsam evaluation to separate function

The bool variable edi->bNeedDoEdsam is used to signal whether any essential
dynamics constraints have to be evaluated for the ED group. This variable
was evaluated at the beginning of an ED simulation in write_edo_legend().
The latter is however not called if continuing from checkpoint. To
get rid of having to remember whether edi->bNeedDoEdsam was already
initialized, there is now a function bNeedDoEdsam(edi) that is evaluated
every time when called.
Also corrected a few typos.

Change-Id: Iab899a677a85ee8270354859c98cc9e5a9db34b7
Pass on default value of radstep in make_edi

This is a bugfix for make_edi when -radfix is chosen. Problem was:
if the user did not specify -radstep, then the default value of 0
was not written to the sam.edi output file. Now it is. Also
renamed "radfix" variable to "radstep" because that better reflects
what it is.

Change-Id: I0cc6ee84d42b18ee0ea6b045cdfb0c1d55d51b9f
cmake: make GMX_BUILD_OWN_FFTW work without fortran compiler

Fixes #1412

Change-Id: I4739c112630ad7e264ce314d2da0b29932ea3041
Merge release-4-6 into master

Conflicts:
Only version:
	CMakeLists.txt
	admin/installguide/installguide.tex
	share/html/online/mdp_opt.html
Other:
	admin/mkhtml (deleted in master)
	cmake/gmxCFlags.cmake (gcc 4.8 change ignored)

Changes other than conflicts:
        src/gromacs/gmxlib/gmx_detect_hardware.c (fix compile errors)

Change-Id: Id5845638857fd84ffaeac618d5286a2d23967f7f