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
Fix indenting of .tpr parameter dump in mdrun log file

This got broken recently in I39550bff60

Fixes #1447

Change-Id: I3e9765e56081d28dd0855d8d8f3fdf39b900993b
Add note about correct calling of wallcycle counter

The code could be refactored to use a series of explicit OpenMP
barriers so that the wallcycle_start/stop are more clearly matched,
but that's too hard for now. The comments make it harder for anyone
to misunderstand or mistakenly change the code.

Change-Id: Iec00e50e26a60efe09afb6f5744d401a9d9c06a3
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
Fix copyright years for new code

These files are new and of code new to GROMACS, so it is
only correct to copyright 2014.

Change-Id: I5d56116f1330fc83380919b111cefa4bf533fb08
Clarified docs for use of mdrun -nstlist

Change-Id: I86118d59116bb183bf81d21bdef8f9c75c12700a
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
Avoid energy drift with verlet-buffer-tolerance

Added a warning with weak coupling and SD when tau_t and
verlet-buffer-tolerance as so large that the temperature might
be off by more than 0.2%.
Turned off nstlist tuning in mdrun with nstlist=1.
Also fixed Andersen checks in mdrun that were useless, since they
were done before temperature coupling groups were set.

Change-Id: I41bd316449c9e03e21d33dd82ebeab034d019fc6
Fix static group list indices in selection prompt

In 4.6, the list was zero-based, and this is what the selection parser
uses when resolving numeric group references, so it should still be.
Also the list shown by various functions in index.c is zero-based.
The printing code had been inadvertently changed to one-based in cleanup
of the handling of group names within the selection code.

Fixes #1506

Change-Id: I9a573b921802d2276e3bdb653359a961c90ff29a
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
Allow trjconv to keep some box dimensions unchanged.

Giving -1 to option box will preserve the original box size
for the given dimension.

Fixes #871.

Change-Id: I339aedcf09da8ecb4eb8f32e8057f953a21e0f5f
Simplified section "Porting".

Fixes #1069.

Change-Id: I01578dfe27585f5c5cc81ce9f564e9586c60a3ed
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
Merge release-5-0 into master

Change-Id: Ibc8f81443d1eaac18b62f544fa149e0924073891