Noting that and why gmxdump -s -sys is broken

Not worth fixing. You could pass a boolean from gmxdump
into the set_posres_params to avoid executing the
problematic line, but that would hit a lot of
other code paths that also call gmx_mtop_to_t_topology.

Refs #635

Change-Id: I308e59287dc578b95ea67c313867df3e75047fa4
Fixing trjconv -sub

The process of making code thread safe broke this.

Change-Id: Ie6617c00e52b09ea0eade2dcb0ae998e8ebf3cc4
Updated code checks with distance restraints

Ensemble-averaged distance restraints require -multi, and it is
also reasonable to do REMD with distance restraints, which also
requires -multi. So checks for the ensemble-averaging case need
to be more sensitive to their context.

In fact, ensemble-averaging is probably functional only with PD and
one processor per system, since that was probably all that was
available when it was built.

Fixes #613, refs #1117

Change-Id: Ia6f1bb4eb82eab3c7c249638cd3a5a5d1f707132
Merge "Noting that and why gmxdump -s -sys is broken" into release-4-5-patches
Merge "Fixing trjconv -sub" into release-4-5-patches
Added fatal error for constraints + L-BFGS minimizer

Refs #1053

Change-Id: I0fd609918927883fc9ec20d0599a48e396d81d94
Velocity-verlet integrators and v-rescale are broken

Added fatal error and suggestion to upgrade GROMACS version.

Fixes #1000

Change-Id: I22653fafdfd0fb2f1fa772fbd95bc55fcf072d8c
Merge "Added fatal error for constraints + L-BFGS minimizer" into release-4-5-patches
Added check for valid wall_atomtype in .mdp

Otherwise, mdrun would dump core when the garbage got dereferenced.

Note that this does not need to be merged into release-4-6, because
c7a82654 already fixes it.

Fixes #700

Change-Id: I39f440595f7b112d4f01b5e32218ec45a2a97370
Fix trjconv -sub with .trr files

ftp is set from the -o file's extension, which cannot be efTRN,
since that's a place-holder file type for command-line parsing.
The error text clearly indicates that .trr (== efTRR) should
work, but of course we have no tests for anything.

Added comment that other trajectory types could work here,
but can't be tested at this time.

Fixes #1118

Change-Id: I118b9b1c25fa7c0640c27e584400dfc64853e67f
Merge "Added check for valid wall_atomtype in .mdp" into release-4-5-patches
Merge "Fix trjconv -sub with .trr files" into release-4-5-patches
Fix reading of g96 title

Change-Id: I5b077ef2f581d704848b658c588636c7510d3c38
Release 4.5.6

- Updated the version to 4.5.6 in CMakeLists.txt, configure.ac
  and gromacs.7
- Regenerated man-pages and completions

Change-Id: I7692220dfe20248b4cdbdd1ed242d1d97f56fda5
Add fftpack to EXTRA_DIST

The new fftpack files added by 51c2f6c are only compiled if
fftpack is used. Thus "make dist" does not included those
by default.

Change-Id: Id51bba3c622a7087f35e74f7c499b066f095fd0d
fix invalid read in construct_vsites

* aj is not available in the F_VSITEN case hence cannot be read in
  the common part of the function

Change-Id: Ic98dfb91eb095aea933abc3dbfb4f5cc10bf4166
Plain text quotes.

And removed 5 gurgles and 2 bromacses - replaced the bromacses
by new and exciting ones.
Change-Id: Ibdad70d6ceb0caa52be351762704a677e9dddba8
Bump shared object version to 7

Almost certainly the ABI is binary incompatible for the 4.5.5 -> 4.5.6
transition, but we didn't think of handling the issue at the time.
So we can do so now.

Refs #1147

Change-Id: I15f978547d7fbcc9a72454067825c71c0ffb459a
Merge branch 'release-4-5-patches' into comp_el