gromacs-5.1.0 beta patch

related to #113

it should works, but more tests are needed

(cherry picked from commit e1d01e84)

This allows one to create information on the differences in
the various patching procedures by executing:

plumed patch -i

This information is also put into the online manual

(cherry picked from commit a273bb84)

This allows one to create information on the differences in
the various patching procedures by executing:

plumed patch -i

This information is also put into the online manual

Old patches have been remove.

Energy was not calculated at every step. Now, gromacs ask to plumed
whether energy is needed at that step and calculate it accordingly.

I also updated the patch to 4.6.1

- the patch.sh and src/lib/Makefile are the same of those in the branch tmp-cmake

the CMAKE patch works different from the former gromacs patches:

- untar gromacs-4.6b3 (./gromacs-4.6/)
- in gromacs-4.6/ copy patch.sh and patch
- mkdir a build folder ./gromacs-4.6/gmx-plumed/
- in gmx-plumed/ run cmake ../ to configure gromacs
- make / make install as usual

there is a bug somewhere for which a "-l" is added before
Accelerate in "-framework Accelerate" thus resulting in a
compilation error.

This is the draft version that I prepared and that we will use as
a starting point. Still it is a bit dirty, and I will try to improve
documentation and delete unused routines