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
Run regressiontests from build

If either REGRESSIONTEST_PATH or REGRESSIONTEST_DOWNLOAD is set,
the regressiontests are run as ctests. The later option auto-
downloads the regressiontest repo.

The "check" target builds and runs tests in one step.
The "gmxtests" target builds tests.
If neither variable is set by the user, the commit doesn't change
the prior behavior (no messsages). Running the new target "check"
without either variable set, prints a warnings.

This commit also removes the prior pseudo test of running
"mdrun -h".

Change-Id: I103648f8a87891727a70775b19449fc269002a1c
fixed SD+BD integration slowing down with OpenMP threads

The SD and BD integrators would integrate on all OpenMP threads,
making the integration much slower instead of faster.
It is not clear if the results could be affected by this bug.
Fixes #1121

Change-Id: Iea4283e0470b72f6f927cb49503ac91d65025647
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 branch 'release-4-5-patches' into release-4-6

Conflicts:
	src/gmxlib/disre.c
	src/kernel/runner.c
	src/mdlib/minimize.c
	src/tools/gmx_membed.c

Change-Id: I1d5f72a3a9b8468cf478890791bc67d247c1e2c5
BlueGene/Q installation notes

Change-Id: I930b316c549dea3ec69ce331bbf9d3dcf0bcd4a9
Merge changes I930b316c,Iea4283e0,I103648f8 into release-4-6

* changes:
  BlueGene/Q installation notes
  fixed SD+BD integration slowing down with OpenMP threads
  Run regressiontests from build
Merge "Merge branch 'release-4-5-patches' into release-4-6" into release-4-6