Neighbor list in multicolvar now has three input parameters

TOL - all values less than this are ignored
NL_TOL - all values less than this are ignored until next neighbor list time
NL_STRIDE - frequency with which to update neighbor list

Neighbor list has been tested for DISTANCES and ANGLES.  Still needs more
testing

Closes #14

The interface to set replica communicator from fortran was missing.

I set it to 2 instead of 2.0, so that it will not be necessary
to update it

gro and xyz files can be written with a requested precision.
Notice that gro files produced in this way do not satisfy the official
documentation of gro format, but still work with e.g. vmd, gromacs,
and plumed driver

Closes #36

It just prints a meaningful error.

This will simplify merging between branches with changes in
the gromacs patch

file the residues they use.

I added a new mode to store patches. If one saves them with
--save-originals (instead of -s) what happens is that
/patches/codename.diff
will be a directory. Instead of storing diff files there,
we will store original/modified pairs.

When patching, if a directory is found in
/patches/codename.diff
the diff are computed and then reapplied on the actual files.

The only change is that the diff is not stored but re-computed on-the-fly.
This has a completely equivalent effect of the original way.
E.g., one can patch two slightly different versions
of an MD code with the same patch.

However, it has the advantage that stored files are more friendly.
E.g., one could directly edit them. Also the git-merge of two
different patches should work better now.

To be consistent with the paper, plumed is always capital letters.
I also changed 2.0 -> 2 and 1.0 -> 1 for sake of generality

I added the possibility to avoid copy of atom coordinates for specific
Actions. Since WHOLEMOLECULES is accessing to atoms in a special manner,
it is now faster.

Without STORE_GRIDS it is necessary to flush the grid file,
otherwise it might stay empty for the entire simulation