Fixed a typo in the manual.

Using > in Latex text mode gave an upside-down question mark instead...
Also used math mode in expression before, which seems more appropriate.

Change-Id: Iefce4768545e899e922e4fa932c67d222927cefe
Added PBC note to comm-mode=angular warning

Change-Id: Id397d51c05512427414aa7decea55fed83ff42ac
Fix group-scheme bug with changing LJ parameters in FE

We don't optimize for the case when we have only changed one of charge
or type, so the other vector must always be valid even when it is not
changing. The logic of calling ewald_LRcorrection didn't do this
correctly, perhaps because the construction logic in md2atoms was
unclear.

Changed name, origin and logic for bFreeEnergy to
bHaveChargeOrTypePerturbed to better reflect the correct usage and
meaning. Avoided testing any pointers for NULL - we should use
explicit control-flow constructs.

Fixes #1596

Change-Id: I61172681048075d3022bd6c4b781c6c9153eeadd
Fixed pull coord init with rate!=0, t_start!=0

When the start time of a simulation is non-zero a pull setup with
coordinates with rate!=0 and pull-start, grompp would generate
incorrect pull init reference values.
Also fixed the layout of the grompp pull coord information table.

Change-Id: I992a40b098853aba0922ec1d596430eb229d64a8
Make tune_pme understand the "-nsteps" option. Fixes #1650

All command line arguments that tune_pme does not understand are passed over
to mdrun. For a quick sanity check the mdrun options are used together with the
additional option "-nsteps 1", which then appears twice on the command line.

The solution is to let tune_pme understand the "-nsteps" argument, so that it
only occurs on the mdrun command line at launch time. The option for that was
already there but before called "-simsteps".

Change-Id: I8362ced75e67b0e28b4a5e1bd427ae6ae4e0e758
Version 5.0.3

Removed -dev tags from versions. Bumped regressiontest hash.

Change-Id: Ieb2588deeb5c866d621af7cbe7e5709ac6f53220
Version bumps after new release

Numbers bumped, -dev tag replaced.

Change-Id: I823a0a79a805c67988a461d891771ff999c6548f
Fix recent bug with trilinic 1D DD

A recent bug-fix (c8d919a3) for triclinic 1D domain decompostion
introduced a bug for boxes with box[YY][XX]!=0.
Fixes #1656.
Refs #1631.

Change-Id: I06b9376212390b73e90a3ce9704dee2bad9693fb
Fix nstep command line override print

The commit addresses two issues:
- printing negative simulation length with "-nsteps -1";
- eliminates rounding when converting a non-integer time-step value from
  fs to ps units.

Fixes #1633

Change-Id: If1aac7e0f4e8e37f3e9777fa4eaa79744f3ccd65
Added grompp error for pulling to negative distance

Change-Id: Ida5f449709c95e7c89cff32957b9e57bc9d68212
Merge release-4-6 into release-5-0

Change-Id: I952a9b8dd61c0eb7456c640997093a1a5fea8fc3
Merge "Merge release-4-6 into release-5-0" into release-5-0
Version 5.0.4

Removed -dev tags from versions. Bumped regressiontest hash.

Change-Id: Idcb1c288b0119c17a9ad644179e96c4734a798f6
Version bumps after new release

Numbers bumped, -dev tag replaced.

Change-Id: I59bbe346656f1892e154f899bac361fcfeea65a1
Merge branch 'release-5-0'

Conflicts:
	CMakeLists.txt
Only changes from version numbers and test hashes, not relevant
for master branch

Change-Id: Ia10e2b82a4ffc3ac408813081c15fe6a858a93f3
Fix cppcheck-1.67 warnings

Remove suppressions for previous cppcheck versions

Change-Id: Ifb03e7b2300b65ca8adb8e22b71da25ea472be52
Merge "Merge branch 'release-5-0'"