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

When not RESTARTing:
file is backed up if existing.
  with STORE_GRIDS, file grows during simulation
  without STORE_GRIDS, file is replaced every time grid is rewritten

When RESTARTing:
  with STORE_GRIDS, file is appended and grows during simulation
  without STORE_GRIDS, file is replaced every time grid is rewritten

This hopefully fixes #34
  

It is possible to print html links to failed tests.
I am setting a nightly build and want to publish online
regtests results

One can know use e.g.
./configure mpi.linux.icc
to directly select the configuration and avoid interactive
choice. Better for building from script

This modification ensures that multicolvar uses less memory and makes
it a tiny bit faster

For a number of complex multicolvars eg. Local_q4 it is useful
to store the quantities calculated in one multicolvar and to use them later.
I had written functionality for this in a somewhat ad hoc manner intially and
as such there was much duplication of code and non uniformity in implications.
This resolves these issues.  Data is now stored more consistently and it is possible
to use a low memory version of this functionality at all times.

This routine no longer made sense in the code