Fixed segfault with FE code for older tpr files.

Full all_lambda array wasn't allocated for gmx 4.5 tpr files, even
though the rest of the code depends on it.

Change-Id: I3e4b6273d9e769a430fffc95e3a9c94fb672f6f3
Document correct comm_mode option

Change-Id: I18d9896c51d486dfcc52e4d15b052d65de91426d
Improved pdb2gmx output

Now there is explicit feedback that pdb2gmx is starting generating
hydrogens and termini, which can help the user deduce that problems
lie with those databases, and not necessarily the residue topology
database.

Change-Id: Ie4100b8586d6389a6965ea8cb09eb24cc4e7d3d9
Update use of CPack components and add install targets

* Removed component runtime and replaced it with component "scripts",
a component for each tool, and the component group tools. This means
CPack is capable of dealing with a single tool, or with the whole
group.
* Moved gmxpreprocess library to libraries component.
* Created CPack dependencies so that shared libraries accompany
executables.
* Created non-CPack install targets for each GROMACS tool, e.g.
"make install-grompp". Shared libraries are installed with these
tools as appropriate. Using library suffices could be right here,
but that's the user's problem to solve.

Development, regression testing and bug testing is more convenient if
you can easily build and install just a subset of tools. This could
always have been done with CMake black magic, but these targets makes
lives easier. Also users can now easily install MPI or
double-precision flavours of selected tools as suitable.

Change-Id: I1053f7ff91d50169ac930f1ac5b84378d3ab2e67
Merge "Improved pdb2gmx output" into release-4-5-patches
Merge "Document correct comm_mode option" into release-4-5-patches
Fixed .g96 trajectory reading.

The line variable in .g96 configuration reading can now be made
persistent - and is done so for reading .g96 trajectories.

This commit fixes #781

Change-Id: If2005a00bb925b41802c4b0dc92e66eb5635f22c
Made tutorial slightly less confusing.

Change-Id: Ief3132a54770e8b3c3b69b24b5582ba321ccc5fd
Don't fail linking if man page building fails

If building of man page fails because binary cannot be
executed (e.g. undetected cross-compile) then fail
silently. A warning is printed when installing.
Only affects deverloper version (not source from cpack).

Change-Id: I9201d44a103602bb26a29b03d14ce08a0089540a
Merge "Fixed .g96 trajectory reading." into release-4-5-patches
Adapted NMR related data to new pdb format.

Since gromacs had adopted the pdb output format to
some standard, the script to convert xplor files
with NMR restratints, such as can be downloaded from
the pdb do not work anymore. The script and accompanying
table have been updated to work with the new pdb format
and simultaneously the extra argument for a residue offset
has been removed. Now the script can be run like
xplor2gmx.pl conf.pdb < restraints.md > disre.itp

Change-Id: I7c3c8bd49b002e2bf0760f4226c913aa36d64611
Corrected REMD citation

The Fukushima paper relates exclusively to MC and spin glasses.

Change-Id: I58c4eafbe41b0cbd1f3e4afac6f34458ed27eea2
Merge "Update use of CPack components and add install targets" into release-4-6
updated references

Change-Id: I74a53433b31c0d50524e0edb5865a8ef9fca1956
Merge "Don't fail linking if man page building fails" into release-4-6
Set valid build information if gmx_detectcpu fails

If gmx_detectcpu failed the error message was written
into the build info which could cause a compiler error.

Change-Id: Id7e367595c14270dc8fa91daa97ce13a4c686057
Fix some memory leaks.

Fixes part of #1004.

Change-Id: I22280999c5c3c40e8efae45461bd53bae8e2ff40
Fixed a deadlock in tMPI_Comm_free()

Fixes a deadlock on overcommitted systems while calling tMPI_Comm_free(),
as first noticed by Roland.

Brings tMPI_Barrier()'s use of atomic variables and memory barriers
in line with the rest of the thread_mpi code.

Change-Id: I86613cdf3c657e907f1168feb544e534889d0557
Backport of md-vv rerun check from c7a82654f2eb8992

Rerun in parallel with md-vv is broken. The check was added
in c7a82654f2eb8992 but also affects 4.5.

Fixes #1003

Change-Id: Ie0e200a8328b2baecd2eba9eea1453c65a668633
fixed recent bug with grompp check for P-R P-coupling

Fix for recent commit 57dac834

Change-Id: I5bc631d6db848c8702a65c42ae27f096804abbf7