Essential dynamics: fixed restarts when ED group has > 1 molecule

To ensure proper restarts when the ED group consists of more than a
single molecule, the PBC-correct positions of the ED group are now
stored in the checkpoint file.

Change-Id: Id87bee610ad248f8695927d0027254e7d6d4c677
Make gmx_cpuid.h self-standing.

The header should now compile irrespective of include order.

Change-Id: I0358b818cdb02ee8a948abc57eed5c4b1a8fdf3c
Minor fixes to g_angle help description.

A few grammatical tweaks and removal of an ambiguous sentence to make
the help description somewhat clearer and more generally applicable.

Change-Id: Ibd2e8a9f43fd81cc1905f06f075f2e43b68bebab
Fixed a bug that with multiple exchanges

Fixed a very subtle bug with multiple exchanges: with multiple
exchanges, Swapping states and swapping configurations are NOT
equivalent, for the same reason that the cycles 1->2->3->1 and
1->3->2->1 are not equivalent.  Also added a number of comments
to help explain the code more.

Change-Id: I52b4543d5b6e1b035d8d6225df3388d0f07cd76f
improved reporting of failed affinity setting

Change-Id: I8a10c524b9d168c29ca587d6328b8d246d287c47
minor speed-up and code clean-up in nbnxn kernels

Clusters without LJ now use the half-LJ instead of the full-LJ
plus Coulomb kernels. This gives a few percent speed-up for water.
Also updated some kernel comments and macros.

Change-Id: Ifa6072561a7042d9d0602ec7d84bc667361951e4
Fixed format error in online manual.

The .gro format indicated a right-aligned residue name, but in
reality the residue name is left-aligned and the atom name in the
next column is right-aligned.  The online manual now reflects this.

Change-Id: I610392c692bf31f962ad069c23d7e55196b64b53
Merge "Minor fixes to g_angle help description." into release-4-6
Removed reference to nonexistent file in g_helix.

For many years, g_helix has referred to a file called n-ahx.xvg, but
no released version of Gromacs has ever produced it. Being that its contents
are largely reproduced by do_dssp, there is no need to introduce this
functionality and thus the easiest solution is to remove the reference
to this file.

Fixes #1103.

Change-Id: I2b87eed44d9d4c174d3772a39abf24827f63202d
Merge "Make gmx_cpuid.h self-standing." into release-4-6
Merge "minor speed-up and code clean-up in nbnxn kernels" into release-4-6
Merge "Essential dynamics: fixed restarts when ED group has > 1 molecule" into release-4-6
Merge "Fixed a bug that with multiple exchanges" into release-4-6
Merge "Fixed format error in online manual." into release-4-6
Merge "improved reporting of failed affinity setting" into release-4-6
Merge "Removed reference to nonexistent file in g_helix." into release-4-6
Merge branch 'release-4-6' into release-4-6-imd