Fixed g_energy Einstein viscosity

The g_energy -vis Einstein viscosity output was obviously incorrect.
This bug has been introduced in version 4.5.
Fixes #1516

Change-Id: I5ffc1a232f0c64769cc438c977b757e8d8b55b98
Updated C-/N-terminal partial charges in Amber03.ff.

At the time of porting the AmberFFs were validated against
AMBER 8 and the results have matched precisely. However,
that specific AMBER version had a bug due to which CT/NT charges in ff03
were in fact using ff94 charges. The bug correspondingly propagated
to the Gromacs ports. In newer versions of AMBER this has been fixed.

The current GROMACS patch uses charges as specified in the
all_aminoct03.lib and all_aminont03.lib files as
taken from the AmberTools14 distribution. 

In that distribution (14) seem to be no updates to the ff9x parameters. 

Fixes #1466.

Change-Id: Ie6cfea5702500ff6cd5019edb22f224d29135425
Fix constraint virial with multiple time stepping

With multiple time stepping the additional nstcalclr-1 force
contribution was constrained to remove it from the virial.
This procedure neglected the non-linear contribution due to
the rotation of constraints. Now the contribution of this force
component to the coordinate update is constrained instead and
the corresponding virial contribution is subtracted from the
constraint virial.

Fixes #1400

Change-Id: If3217f52808bf7491998324f8dc3161bc003ec1b
Merge release-4-6 into release-5-0

Conflicts:
	src/gromacs/gmxana/gmx_energy.c
Eliminated time parameter (removed in release-5-0),
used gmx_ffclose (fixed in release-5-0).

	src/gromacs/mdlib/update.c
Eliminated fplog parameter (removed in release-5-0), otherwise added
new MTS-fixing functionality from release-4-6.

	src/programs/mdrun/md.c
Added new code path for MTS (from release-4-6), eliminated
wcycle and bInitStep parameters (from release-5-0).

Change-Id: I303bb649ed2373656aa4420d0afb27f738a9ea30