Prohibit AVX_256 with buggy gcc 4.6.1

Fixes #1259

Change-Id: I7c523a90ccd0dd8fd3df6cb1914429e22a27ab5d
Fixes a complicated bug in g_anaeig.

If the number of frames for a covariance analysis is fewer than the
number of degrees of freedom, g_covar would happily print nonsense
eigenvalues in the eigenval.xvg file. This would then lead g_anaeig
to give NaN entropy values. By limiting the number of output lines in
the eigenvalue file this should be resolved. In addition a warning is
printed.

Change-Id: I01693a0fa9f3ba5b5784543a04d0d88b33a755c2
Added a note about unsupported Verlet cutoff + Buckingham.

Refs #1192.

Change-Id: I2da3bf8c768de40531e1ffdf6f8cec73c9e53314
Added a note about using direction-periodic pulling.

Refs #1352.

Change-Id: I867fe1372082063bb221880e8021089f9ded14e7
Improvements to the g_lie help description.

Information was sparse, likely to avoid restating published
protocols, but some expansion was definitely warranted,
given the amount of questions that have recently been
posted to the mailing list and Redmine.

Refs #1353

Change-Id: Ib4057ae671ccac70061498b1d40ebcba84c497ee
Add fatal errors for VV and twin-range MTS

Michael never implemented the multiple-time stepping with the VV
integrator family and constraints (see code that calls
combine_forces() from update_coords() in src/mdlib/update.c). Probably
that means the multiple-time-step regime was not tested with VV
either. Strictly speaking, these new fatal errors have scope that is
wider than is clearly warranted, but it is not clear the
no-constraints VV path was only ever as bad as the broken leap-frog
path is (see #1400).

I suspect VV+constraints will work with the incoming fixes for
leap-frog, but until someone wants to use it (and why would they?),
then I'm not going to test that it works as well as it does with
leap-frog.

Change-Id: Ib61d0fb7661bca2101c04423a6af1744420c06ab
Normal modes don't work currently with virtual sites or shells.

Refs #879.

Change-Id: I1c45b5a4b4c97feff222dccbbbb884e0153ad0c5
Fix memory issue in solvate

Caused by SIMD padding introduced by new group kernels.

Fixes #1499

Change-Id: I5126217c9b752f1c1fd04d01e2644987fdc52d5b
Merge release-4-6 into release-5-0

Conflicts:
	CMakeLists.txt - fixed use of GMX_CPU_ACCELERATION
	src/gromacs/gmxana/gmx_lie.c
	src/gromacs/pulling/pull.c

Change-Id: I45a70eee6f7ec4dd922b6c04c740c40f50159a45