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
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
Small fix for g_tune_pme

Setting the "-err" command line flag in g_tune_pme would, in combination with the "-launch" flag
prevent a proper launch of mdrun after tuning since "-err" would also appear on the mdrun
command line. This patch removes the "-err" switch from the mdrun arguments list.

Change-Id: Idb2e3cf2e4eca587180b932faccc227be171b3d7
Fix for the pressure in MTTK with constraints + dispersion

Fix for pressure in MTTK - broken at some point in the
merge process.  The MTTK+constraints code definitely needs to
be simplified for 5.0, it's too easy to break on code rearrangements
right now!

Testing with simple systems over long time shows that the pressure is
unbiased, while the PR pressure is off by a factor of 1/N (which is totally
fine for most realistic systems).

Fixes redmine bug #1061
Change-Id: Ie82cf8d6bdeb3e47db044ae34fc42c077ad73c75
Fixed AVX256 double-precision kernels for gcc

Gcc is pickier with memory alignment and implicit conversions than
either clang or icc. This patch makes sure we align tables to 32-byte
boundaries (16 before), and uses explicit casts to make gcc happy.
Fixes redmine #1074.

Change-Id: I613d49dad74597ce6167e18fd3a048254bc1b859
Fixes for expanded ensemble and HREPEX

Various other fixes broke expanded ensemble and Hamiltoian
replica exchange. These changes restore functionality.

Change-Id: Iae9def3838a5b90f1efee1fb0598441e0af6cce3
Fixes for andersen temperature control

First, fixes a bug introduced in the merge that
caused the same random seed being used on all nodes, resulting
in correlated velocities in the kinetic energy, and thus an
incorrect distribution of total kinetic energy because of correlations
between particles.

Also fixed another bug caused during merge that resulted in andersen
not being applied when there were no constraints.

Change-Id: If6b857bf3d3b9345c18d0680fdba0f65a4860a7e
cmake: added option to disable quotes

Change-Id: Ia1793f3d3dddb3a08012723c2279cab51fa1eafa
Merge "Fixed AVX256 double-precision kernels for gcc" into release-4-6
Merge "Fixes for expanded ensemble and HREPEX" into release-4-6
Merge "Fixes for andersen temperature control" into release-4-6
Merge "Small fix for g_tune_pme" into release-4-6
Merge "cmake: added option to disable quotes" into release-4-6
fix incorrect gmx_fatal argument order

The format specifiers did not match the argument order.

Change-Id: Ib58892f4b0e09d7c3d3442a88f0bda98ea4b54b9
Remove non-functional compiler override for MacOSX.

As discussed in #1021, at least with CMake 2.8.9 this does not work, so
it only causes confusion.  A better solution can be implemented if
identified in #1021 discussion.

Related to #1021.

Change-Id: Iec704dcae65cd7a213cf31861a262ac0b2763474
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
Make gmx_cpuid.h self-standing.

The header should now compile irrespective of include order.

Change-Id: I0358b818cdb02ee8a948abc57eed5c4b1a8fdf3c
Fixed gmx_cpuid not working on non-x86

Added x86-specific #ifdefs around calls to x86-specific routines.
The cpuid calls should now correctly return 'unknown' for everything
on other platforms. Fixes #1075.

Change-Id: Id0dfcb2fd944ea37b176efb9978ccedfc00e06e9
Merge "Remove non-functional compiler override for MacOSX." into release-4-6