Print out atom numbers in g_rmsf

Reasonable output of g_rmsf would be the atom numbers
and not the group indices.

Fixes #893

Change-Id: I16a8e25f1934ef40952f24ffd5ab835acabfff72
Minor spelling&header fixes for various man pages

see: http://patch-tracker.debian.org/patch/series/view/gromacs/4.5.5-2/31_manpages.patch

Change-Id: I813ed653b9b50125652fef5522a51304773414dc
Ignore bool cast warning for MSVC and C++

We have been ignoring this warning for C++ in master for a while.
No need for it for the GPU code either.

Change-Id: Ib76541d344dc520d5a14da241b29d92362311980
[tools] g_sans - add trajectory avereging

This change adds
1. trajectory averaging for s(q) and p(r)
2. can compute s(q) and p(r) for each frame

Change-Id: Ieb421a8b5ae06b72442bbe5fbae4231a7fa9c980
Signed-off-by: Alexey Shvetsov <alexxy@omrb.pnpi.spb.ru>
Remove superfluous memory allocation.

The next line allocates the memory again.

Fixes #918.

Change-Id: I6f727cf059ccdc5d407b8398b9b29db625c120b8
cmake: remove double-negative quotes logic

Change-Id: I75b3a45a4f0fbbff6300a6317126c5b0cc302b86
Merge "Ignore bool cast warning for MSVC and C++" into release-4-6
fixed nbnxn AVX-256 Ewald table pointer alignment

This could lead to access violations, but up till now
this was only observed with 32-bit MSVC builds.
Fixes #1097

Also added more documentation to nbnxn_kernel_simd_utils.h,
renamed macro variables and added minor table optimization
by replacing shuffle with movelh or unpack.

Change-Id: I9df2131cbabb0e6cb86f7224a5fd238acb2e7681
Fix CUDA being quiet and mark all CUDA_* as advanced

The if statement was wrong (didn't agree with comment) and caused
FindCUDA not to be quite on the first run. Also one of the
FindCUDA varaibles CUDA_TOOLKIT_ROOT_DIR wasn't marked as advanced.
While that one is the most important variable, similar variables
(e.g. ${FFTW}_LIBRARIES) is also advanced. It is only marked as
advanced if NOT GMX_GPU.

Fixes #1088

Change-Id: Id6d2c16e64688f1dd4bb3193017deb8b36c5c06e
Merge "Print out atom numbers in g_rmsf" into release-4-5-patches
Merge "cmake: remove double-negative quotes logic" into release-4-6
Reduce use of monolithic sets of compiler flags

This prepares to fix the Redmine issue below (but perhaps could
be folded into it).

Refs #1038

Change-Id: I6407dbbd331e58c30ab1b275748a211040c9c414
Merge "fixed nbnxn AVX-256 Ewald table pointer alignment" into release-4-6
Merge "Reduce use of monolithic sets of compiler flags" into release-4-6
Do not always add -msse2 to release flags for icc

At least on Windows, this flag will override the -msse4.1 or -mavx
flags added to the main C flags. Since we already add -msse2 in
the same place when using SSE2, I see no reason why it should be
added to the release flags separately.

Change-Id: I933f5b1d5e4e4ead1635ec47b5272a0f6f69da67
Add check to remove zero Charmm dihedrals

Proper torsions where the force constant is zero
in both A and B states are now removed. We also
check for other angle, torsion, and restraint
functional types, and if all parameters are zero
for these the interaction is not added. This will
not change any results, but increase performance
slightly by not calculating unnecessary interactions.
Fixes #810.

Change-Id: I37ecd06d0641008593edab29e5b08433bde7b6cc
Added work-around for gcc bug in AVX intrinsincs formal parameter

Many relatively recent gcc versions (4.5.2, possibly 4.6.0) use incorrect
formal parameters for maskload and maskstore intrinsics. This patch
detects the bug during configuration and works around it with a define.
Refs #1058, and fixes it at least from gcc-4.5.2.

Change-Id: I447a968d2153f5acf59ad170ace69ad1b6b3f24d
Merge "[tools] g_sans - add trajectory avereging" into release-4-6
Merge "Add check to remove zero Charmm dihedrals" into release-4-6
Merge "Added work-around for gcc bug in AVX intrinsincs formal parameter" into release-4-6