Implemented fast weighted alignment with align!=displace

In this version the fast routine is hard-coded. I do not compute explicitly the derivatives of the rotational matrix.
Instead, I assume them to be zero and at the end add a contribution which resets total "force" and "torque" (i.e.
I enforce translational and rotational invariance of the RMSD). In test rt47/check one can appreciate that
numerical derivatives come out correct. I do not know exactly why...
Added internal lapack/blas

Adapted from GROMACS
missing regtest
libmolfile plugin in driver
test for molfile_plugin
added rt2
Missing malloc. Thanks to Toni
Merge branch 'v2.0' into internal-lapack
Merge branch 'v2.0' into internal-lapack
Fixed configuration file)
(suggested by Toni Giorgino)
Merge branch 'v2.0' into internal-lapack
Fixed automatic backbone detection for secondary structure variables

The nature of the backbone is now specified by a class called MolDataClass.
A warning is given about GLY residues
Added functionality to read torsions for proteins using psi-4 or phi-6
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
Improved RMSD with align!=displace

I did it in the boring way - full derivatives of rotation matrix.
It seems to work now, but still breaks some test. It is probably
some numerical issue, I will investigate before merging.

It is slower than the align==displace version (~ a factor 1.5),
but I think it is more than acceptable.