Avoid stack overflow on Windows with CMake > 2.8.10.2

CMake used to add "/STACK:10000000" to the default linker flags. That
was removed in version 2.8.11-rc1. The default value used by MSVC is
apparently too small because mdrun crashes with a stack overflow when
built on Windows with MSVC or ICC and CMake newer than 2.8.10.2.

The issue is already fixed in GROMACS 5.0 and master by I1e9858ae3. This
is a backport for release-4-6 of that commit.

Change-Id: Ib9238e513da8e86049d9e56c82262055d3c8b349
Fixed output of eigenvalues in g_covar. Fixes #1575

Commit 972032bfb8cd38 introduced a bug that would lead to eigenvalues
only written to .xvg file if "-last" is explicitly stated on the
command line. Otherwise no eigenvalues would appear in the .xvg file.
The eigenvalues are written in a loop from '0' to 'end', but since
'end' is initialized with '-1', the loop would never be executed.
This patch moves the code that computes 'end' one block upwards
before the output to file.

Change-Id: I738c9dd77ff9e6e2daae89b6d2063755dfba88af
Fixed bugs in vsiteN with OpenMP

Fixes #1579.

Change-Id: I42d234f4ad6a94e8f7b6b8236ea119860dd9f7ab
Fixed two PME issues with MPI+OpenMP

Change 272736bc partially fixed #1388, but broke the more general
case of multiple MPI communication pulses in PME. Change 272736bc
incorrectly changed tx1 and ty1. This change has been reverted.

Change 27189bba fixed the incorrect PME grid reduction with multiple
thread grid overlap in y. But it broke the, much more common, case
where the y-size of the PME grid is not divisible by the domains in y.
This change, incorrectly, changed buf_my.

Now buf_my is set to the correct value, which solves both issues.

Fixes #1578.
Refs #1388 and #1572.

Change-Id: Id2d7d013a3b8cdc04eda1fb026567088a38ec81f
Merge branch release-4-6 into release-5-0

Conflicts:
	src/gromacs/fileio/gmxfio.c
Used new release-4-6 code calling renamed md5 functions

	src/gromacs/gmxana/gmx_covar.c
Used gmx_ffclose, not ffclose, for file opened with xvgropen.

Change-Id: If6f9cb61bf7eab06dfdc61a03ad89ed38d599382
Merge "Merge branch release-4-6 into release-5-0" into release-5-0