cppcheck warnings

This commit contains changes automatically generated by plumedbot on Travis-ci.

Copying standard vectors out of grid is very slow if you use it intensively

You can now use COLLECT_FRAMES to collect pdb data from the trajectory
and output a pdb file that contains the underlying atomic coordinates
in pdb format even if you are not using the rmsd distance to measure
the dissimilarity matrix for dimensionality reduction.  Also fixed
a number of bugs.

I have moved mds from the analysis module to a separate dimred module
as I think it is best to keep this with the other dimensionality
reduction algorithms.  It is now default off though