/**
\mainpage Introduction

PLUMED is a plugin that works with a large number of molecular dynamics codes (\ref codes). 
It can be used to analyse features of the dynamics on-the-fly or to perform a wide variety of free energy methods.
PLUMED can also work as a \ref tools to perform analysis on trajectories saved in most of the
existing formats. If PLUMED is useful for your work please read and cite \cite plumed2, if you are interested in 
the PLUMED 1 original publication please read and cite \cite plumed1 .

To follow the development of PLUMED 2, you can look at the detailed \ref Changelog .

To install PLUMED, see this page: \ref Installation , while in \ref Syntax you can find a brief introduction on how to write your first PLUMED input file.

\ref tutorials are available to introduce basic as well as more advanced features of PLUMED.
 
\section AboutManual About this manual

@VERSION@

This is the user manual -  if you want to modify PLUMED or to understand how it works internally, have a look at the 
<a href="../../developer-doc/html/index.html"> developer manual </a>.

@PDFMANUAL@

\section codes Codes interfaced with PLUMED 

PLUMED can be incorporated into an MD code and used to analyse or bias a molecular dynamics run on the fly.
Some MD code could already include calls to the PLUMED library
and be PLUMED-ready in its original distribution.
As far as we know, the following MD codes can be used with PLUMED out of the box:
- [AmberTools](http://ambermd.org/), sander module, since version 15.
- [CP2K](http://www.cp2k.org), since Feb 2015.
- [ESPResSo](http://espressomd.org), in a Plumedized version that can be found
  [here](http://davidebr.github.io/espresso/).
- [PINY-MD](http://github.com/TuckermanGroup/PINY), in its plumed branch.
- [IPHIGENIE](http://sourceforge.net/projects/iphigenie/).
- [AceMD](http://www.multiscalelab.org/acemd/), see [this link](https://github.com/tonigi/ACEMD-PLUMED).
- [OpenMM](http://openmm.org), using the [openmmp-plumed plugin](http://github.com/peastman/openmm-plumed).
- [DL_POLY4](http://www.scd.stfc.ac.uk//research/app/ccg/software/DL_POLY/44516.aspx).

Please refer to the documentation of the MD code to know how to use it with the latest PLUMED release.
If you maintain another MD code that is PLUMED-ready let us know and we will add it to this list.

Additionally, we provide patching procedures for the following codes:

@CODESL@

Alternatively, one
can use PLUMED as a \ref tools for postprocessing the results from molecular dynamics 
or enhanced sampling calculations.  Notice that PLUMED can be used as an analysis tool
also from the following packages:
- [PLUMED-GUI](http://github.com/tonigi/vmd_plumed) is a [VMD](http://www.ks.uiuc.edu/Research/vmd/) plugin that computes PLUMED collective variables.
- [HTMD](http://www.htmd.org/) can use PLUMED collective variables for analysis.

\page Changelog Change Log

Here you can find a history of changes across different PLUMED versions.
The future releases are expected to follow more or less the pace
of the old release. This means:
- Approximately once per year, after summer, a new release (2.X). These releases
  typically group together all the features that were contributed during the
  year.
- Approximately every three month, we announce a patch (e.g. 2.2.X).
  This typically contains bug fixes, and could occasionally contain a new feature.

A few months before each new release we provide a beta release.
We typically maintain release branches until the fifth patch release (2.X.5),
which should come out approximately 15 month after the original release (2.X).
After that, branches are not supported anymore.

Notice that occasionally we publish patches on the mailing list.
These patches are always included in the following release, but we encourage
users that want to be up to date to follow the mailing list.

Below you can find change logs for all the published releases.
We mostly add new features without breaking existing ones.
However, some of the changes lead to incompatible behavior.
In the Change Log we try to give as much visibility as possible to these changes
to avoid surprises.

We also log changes that are relevant if you are developing the code. These
change lists are however not complete, and if you want to put your hands in the code
and maintain your own collective variables we suggest you to follow the development
on github.

@CHANGES@

*/