Keep CMake quiet about a Cygwin issue

The CMake warning that is suppressed by this does not affect GROMACS
builds.

Change-Id: I6a19f55868b6363cb2be328286b4716659cc270b
Improved pdb2gmx error message

Increased the extent to which pdb2gmx makes use of the encapsulation
available with the t_atoms struct. Now the function that writes the
error message has an easier time being more descriptive of what
is wrong when the atoms in the input coordinate file do not match
those of the .rtp entry.

Change-Id: Ie39dea18efa358f90decad6491ddc04e3756ac39
Merge "Improved pdb2gmx error message" into release-4-5-patches
Fixes problems with g_msd and g_energy

* Fixes a problem where g_msd will stall on reading a file
  with xy periodic boxes.

* Fixes a problem with gmx_energy ignoring the -skip option.
  Was correct in 4.0.7, but was wrong by 4.5.5. Redmine issue #910

Change-Id: I4247a4bd1cf1ab15ea6157646c97452216a887aa
Merge "Fixes problems with g_msd and g_energy" into release-4-5-patches
Merge remote-tracking branch 'gerrit/release-4-5-patches' into release-4-6

Conflicts:
	CMakeLists.txt

Change-Id: I67d65e260f68442841d8b901d77780b8d1505340
Fix domain decomposition setup for >46k cores

Fixing int overflow in line 701:
  ldiv*ldiv*ldiv > nnodes_div*nnodes_div

Change-Id: Ic97960caededeee255e874b81d9bbd2fc71d2ae6
Consolidated documentation of .mdp restraint options

Change-Id: I04164a0e9a36338c5e412cdf73da78ef58299920
Merge "Consolidated documentation of .mdp restraint options" into release-4-5-patches
Lots of manual updates

Accompanies changes in the manual project

Change-Id: I4c64d660f2a0dc2c265efb2f983d4ffbaf432fd4
Documentation and error message enhancements

Change-Id: I4282e37c6b070607351cdafba56441b43fb04cd1
Merge "Documentation and error message enhancements" into release-4-5-patches
Permit threads build on Cygwin

Fixes #833
Change-Id: I1429629417132c164e9b017721c0035583d7d6bf
Made g_helix sensitive to CHARMM atom naming

Peptide N-H atoms named HN in CHARMM were not recognized as backbone
atoms.

Fixes #896

Change-Id: I205b8dc5c895f20e6cde61ee2a1640fc6414b030
Introduce include/gmxconfig.h

This header file is for #defines that should be available in an installed
header file that can be used by projects that depend on GROMACS. The
src/config.h used in building GROMACS is not installed, and so is not
available to such projects. CMake is used to configure
include/gmxconfig.h.cmakein and create include/gmxconfig.h.

Change-Id: Ide36fb4c0958d5faa647263411b3cfb91baa1d61
Fix that directory is not mistaken for binary

The smart searching for the library path searched for an existing
inode with the name of the binary. If a directory with that name
existed, it was mistaken for the binary.

E.g.:
$ mkdir pdb2gmx
$ pdb2gmx
Fatal error:
No force fields found

This patch replaces gmx_fexist with gmx_is_file which checks that
the inode with the name of the binary is not a directory.

Change-Id: I78cdf8136db9ed69b75dcb1d4d0582ab388ef1d8
Reworked FindFFTW.cmake

* make user input FFTW_{LIBRARY|INCLUDE_DIR} work and advanced
* ade more documentation
* reconsider test if failed in the last run
* improve error messages to the user
* check if fftw is compiled with sse support
* fixed detection on Cray

Change-Id: I0b7d440d372da7cf897ca956ccd882e21b109591
Read PDB information in read_tps_conf().

Fixes #916.

Change-Id: Iaa2bed444b632b4596c6a4e9a4c527a6bc0236b8
Clarified warning string

Change-Id: I65d422d342b946a548e9a29234d1803a13b1a9f0
Clarified warning message

Change-Id: I6fb5ba3cc42604e2445b4cb48093227478e6a613