Notice that as of now it is not fully integrated in the plumed
reference/ module. However, it is possible to compute
ERMSD from a given structure and to use it as a CV

[makedoc]

Changes were also needed as this feature was broken as a consequence
of changes in no-buffer branch.  Change to dynamic list deletes
a check that is active when you compile with -DNDEBUG that is not really needed

Allows to specify residues with chain id as letter, e.g.
phi-A102

No letter implies first chain

Fix #133

There were some problems with the documentation generation in SPRINT
that are now fixed.  Some routines in MultiReferenceBase were not in
a very sensible place.  I also changed PDB so that you can add stuff
to the remarks.

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

The nature of the backbone is now specified by a class called MolDataClass.
A warning is given about GLY residues

This involved splitting the code for reading an argument list from the code
for interpretting it, adding a function for reading the ARG argument from the pdb and
interpretting things like ARG=d1.* to ActionWithArgument and adding a routine
to PDB which allows you to replace the old ARG=d1.* with the newly interpretted
ARG=d1.x,d1.y,d1.z

If you want to but a plumed_assert in a loop you should now use
plumed_dbg_assert / plumed_dbg_massert.  This will not be included
in the code if you compile with -DNDEBUG

All the source code have been moved into subdirectories of src/
Some of these subdirectories are treated in a special manner:
src/wrapper contains the wrappers for MD codes
src/main contains the main.cpp file
src/config contains files generated without compilation,
  just based on configuration info
src/lib is the place where executables and libraries are put
  at the end
src/cltools contains the command line tools
src/tools contains plumed tools (reusable classes)
src/basic contains PlumedMain, Action hierarchy and other basic stuff
src/multicolvar contains MultiColvar stuff
src/imd is the interactive MD (still not totally portable).

Notice that, to allow easy inclusion of .h files from other modules,
I link all the directories in src/ into module directory. In this
way it is possible e.g. to write #include "config/PlumedConfig.h"

See src/README and src/basic/Makefile to understand how inter-module
dependencies are set

Detected with -pedantic

when it is required. Code returns an error if it is not there.
This is an easy mistake to make but previously if it was made one
only got a segfault.

as suggested by Gareth

I added a PEOPLE file containing list of authors and a script
(src/header.sh) which applies the Licence to all the source files.

It can be applies multiple times (it automatically deletes the present header
and replace it with the new one). Thus, to change the header, edit header.sh
and execute it.

Also got rid of the stuff on beta sheet between chains as I wasn't
sure how to make it work

in terms of the residues for the chains for which one wishes to calculate the distances
from the alpha helical secondary structure.  For these reasons I had to adjust the PDB
parser so that it reads in atom symbol, resdiue and chainID data.  I then I have an
ActionSetup class (MolInfo) that can read and store the data on the various chains inside the
pdb file.  I have that you can calculate the distances from the secondary structure using either
DRMSD (like plumed 1.0) or using Davide's RMSD class.  This required a very small change to Davide's
RMSD class.

The point in CV space can be specified using a pdb file, hence the changes
to Action, Value, etc - all these changes are all so that you can calculate CVs from a
pdb input file.  Whilst I was messing about I noticed a potential problem with
natural units and input pdb files.  As we are in natural units there is no
way of knowing how to convert the pdb from angstroms (unit in pdb)
to the natural length unit.  For these reasons I assume that when one is in
natural units pdb input files are also in natural units, this required changes
in ColvarRMSD and my new ColvarTarget routine as well as a small change in Atom.h.

I removed scale method from Vector. I think it is
more readable to use the *= operator.