Release 4.5.6

- Updated the version to 4.5.6 in CMakeLists.txt, configure.ac
  and gromacs.7
- Regenerated man-pages and completions

Change-Id: I7692220dfe20248b4cdbdd1ed242d1d97f56fda5
Add fftpack to EXTRA_DIST

The new fftpack files added by 51c2f6c are only compiled if
fftpack is used. Thus "make dist" does not included those
by default.

Change-Id: Id51bba3c622a7087f35e74f7c499b066f095fd0d
fix invalid read in construct_vsites

* aj is not available in the F_VSITEN case hence cannot be read in
  the common part of the function

Change-Id: Ic98dfb91eb095aea933abc3dbfb4f5cc10bf4166
Plain text quotes.

And removed 5 gurgles and 2 bromacses - replaced the bromacses
by new and exciting ones.
Change-Id: Ibdad70d6ceb0caa52be351762704a677e9dddba8
Merge release-4-5-patches into release-4-6

Avoided the 4.5.6 release patch by using
git merge -s ours 10b109beb3ffa95e37386d38140d2c0fd7769f20
git merge release-4-5-patches
tree=$(git log -1 HEAD --pretty=%T)
git reset --hard $(git cat-file commit HEAD | sed '1,/^$/d' | \
    git commit-tree $tree -p 2b05689 -p 8d6cc14)
Conflict resolution was straightforward, except that the vsite
code was somewhat reorganized in the meantime.

Conflicts:
        Makefile.am
        src/contrib/Makefile.am
        src/contrib/addquote.c
        src/gmxlib/copyrite.c
        src/mdlib/vsite.c

Change-Id: Ib90ac4e55fac308c433b15c344caf5ee41f0146c
fixed issues with FEP soft-core and cut-off's

Now the cut-off is applied to the PME mesh correction for perturbed
pairs with soft-core. Now the cut-off is applied to VdW with soft-core.
Fixes possible NaN in free energy kernel with r close to 0.
Replaced a confusing grompp warning with PME and soft-core by a note.
Removed an invalid grompp warning about soft-core and twin-range.
Fixes #1146

Change-Id: I79a06b20158df2bce575808b6e31e660163bd307
Bump shared object version to 8

libs are not compatible with the ones from Gromacs 4.5.x, which had so
version 6 through 4.5.6, and now so version 7 for 4.5.7.

Fixes #1147

Change-Id: If96fd044b00a99eb4ba8376ffa0a2ecbea37894a
fix imcompatibility with tpr vers<64 with free energy option

should fix to redmine #1156

Change-Id: I6e60f1efbb03bf460009b8bc59f80f2e0e15bf44
Uncrustified code changes since 4.6

The group kernel python scripts have changed slightly to emit
code that uncrustify won't want to change. Group kernel
generation and uncrustify are now mutual null operations.

Recent changes to the declarations in gmx_order in baa65b60
may have exposed a possible bug in uncrustify. Those declarations
have been simplified so that there will be no future issue from
that possible bug.

Refs #845

Change-Id: I33495d57ca37317cef4bf12707fd77d67309d292
fixed PME time print with -ntomp_pme != -ntomp

Fixes #1158

Change-Id: I9028e6309b8802125e91935e87d96b341ec30f77
Declaration-definition consistency nbxn_cuda_wait_gpu.

Changed float->real in nbnxn_cuda_wait_gpu() for consistency between
function declaration and function definition.  Added note that this is
only implemented for single-precision at the moment.  CMake will
complain if GMX_GPU and GMX_DOUBLE are both set.
Addresses Bug #1157.

Change-Id: Ide495cbaba6d120d91f106c6a87ca04e46a2f5a8
Merge "Uncrustified code changes since 4.6" into release-4-6
fix broken things in mkhtml

Change-Id: Ifb9aa694eddd4bffe457674265a2b17093182c50
Warn if X11 was not found and the user wanted it

Also, removed unused HAVE_X11 variable.

Change-Id: I581b2036f9de27a02c034230f2d1212b9814ffbb
Updated install guide

* bumped some versions for 4.6.1
* reviewed various promises about 4.6.1

Change-Id: I6d8549e1f47c53367db275c3091b02556af3b8d8
Fixes for install guide page.

Editorial fixes to rename GMX_LIBS_SUFFIX and provide an example
of proper usage of adding suffixes.  These edits now keep the .tex
file in sync with the edits manually made to the wiki page.

Change-Id: Iba5b4c66ad3d0d84ddb06591d4681ff48e4de2ee
Fixes linkage with FFTW + MKL for BLAS/LAPACK

The order of linking was incorrect, when using both mkl and fftw
causing the mkl fftw wrapper to be used instead of fftw itself.

Removes all unnecessary transitive libraries (cmake adds those
automatically). Simplifies the target_link_libraries lines, and
makes it much easier to change the fft/blas link order.

Only remaining transitive libraries are gmx/md for binaries. This
is required because OpenMP_LINKER_FLAGS needs to be at the end
but transitive libraries are added at the end. Thus without listing
gmx/md manually the order is incorrect.

Also fixes that nbnxn_cuda has cuda_tools listed as library
dependency. Was prior working without it but now is needed and is
also anyhow the more corect way to do it.

Fixes #1067

Change-Id: I639b16f1460d27a15eb72cc00674c041266f6624
Update outdated admin things

* remove outdated CMake installation guide
* updated the bootstrap script
* remove outdated admin/README.patches
* update README, including adding reference to
  GROMACS 4.5 paper and DOIs for old papers

Change-Id: I9a55126049806ca67f6ad846cdbd67cc530c7db0
Update shell completions

There's some strange changes of what completions are being generated
for inputs that take multiple files when generated by different 4.6.x
versions, but nobody seems to know what is going on. Also, those
problems do not have a large impact.

Refs #1159

Change-Id: Ib4b1ad4999e1b68904d46b0d01c2a5dd07507fd7
fixed recent bug with sorting atoms for GPUs

The sort buffer in the nbnxn gridding for GPUs was made too small
in 8d6cc146. This led to inconsistency errors (not incorrect output).
This is fixed and the sort_atoms call is now made simpler and
multiple consistency checks are now always on in debug builds.
Fixes #1153

Change-Id: Ifcdf45bb4de88e7584628d3ed2699e2fd469d5c6