Experimental gromacs patch with better GPU balancing

When ENERGY CV is not used, plumed calculation is done
on the CPU at the same time as nonbonded evaluation on the
GPU. This allows to better exploit load balancing.

Since it also patches src/mdlib/force.c, it does not
allows to compile anything in gromacs besides mdrun.
Merge branch 'v2.0' into v2.0-gpu-balance
Merge branch 'v2.0' into v2.0-gpu-balance
All the tools compile properly now
Merge branch 'v2.0-save-originals' into v2.0-gpu-balance

        To solve conflicts I had to recreate the patch.
        I did this:
        1. patched gromacs with v2.0-gpu-balance
        2. merged v2.0-save-originals
        3. saved diff file
        4. git mv gromacs-4.6.3.diff gromacs-4.6.3.diff.tmp
        5. git rm gromacs-4.6.3.diff
        6. git mv gromacs-4.6.3.diff.tmp gromacs-4.6.3.diff
        7. git add gromacs-4.6.3.diff

        Future merges should go smoothly.

Conflicts:
	patches/gromacs-4.6.3.diff
Merge tag 'v2.0.0' into v2.0-gpu-balance
Merge branch 'v2.0' into v2.0-gpu-balance
Merge tag 'v2.0.1' into v2.0-gpu-balance
Merge branch 'v2.0' into v2.0-gpu-balance
Merge branch 'v2.0' into v2.0-gpu-balance

Also moved
gromacs-4.6.3.diff/src/mdlib/force.c*
to
gromacs-4.6.5.diff/src/mdlib/force.c*
Merge branch 'v2.0-gpu-balance' into v2.0

Merged a branch with a modified gromacs 4.6 patch which
allows for better load balancing when using gromacs
with GPUs.
changelog
Merge branch 'v2.0'

Small fix needed due to the fact that master branch
also calls cmd("setStopFlag") (for committor analysis)

Conflicts:
	patches/gromacs-4.6.5.diff/src/kernel/md.c