Intro.txt

/**
\mainpage Introduction

PLUMED is a plugin that works with a large number of molecular dynamics codes.  It can be used
to analyse features of the dynamics on-the-fly or to perform a wide variety of free energy methods.
The original PLUMED 1 \cite plumed1
was highly successful and had over 1000 users.  PLUMED 2 \cite plumed2 constitues an 
extensive rewrite of the original in a way that makes it more modular and thus easier to implement 
new methods, more straightforward to add it to MD codes and hopefully simpler to use.  
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>.

\htmlonly
An experimental PDF copy of this manual can be found
<a href="../manual.pdf"> here </a>.
\endhtmlonly

To understand the difference between PLUMED 1 and PLUMED 2, and to
follow the development of PLUMED 2, you can look at the detailed \ref Changelog.

A short tutorial explaining how to move from PLUMED 1 to PLUMED 2 is also available (see \ref moving)

To install PLUMED 2, see this page: \ref Installation

\section AboutManual About this manual

@VERSION@

Since version 2.1 we provide an experimental PDF manual.
The PDF version is still not complete and has some known issue (e.g. some
links are not working properly and images are not correctly included),
and the html documentation should be considered as the official one.
The goal of the PDF manual is to allow people to download a full copy on the documentation for offline
access and to perform easily full-text searches.
Notice that the manual is updated very frequently (sometime more than once per week),
so keep your local version of the PDF manual up to date. 
Since the PDF manual is 200+ pages and is continuously updated,
<b>
please do not print it!
</b>

\section qintro A quick introduction

To run PLUMED 2 you need to provide one input file.  In this file you specify what it
is that PLUMED should do during the course of the run.  Typically this will involve calculating 
one or more collective variables, perhaps calculating a function of these CVs
 and then doing some analysis of values of your collective variables/functions or running
some free energy method. A very brief introduction to the syntax used in the PLUMED input file
is provided in this <a href="http://www.youtube.com/watch?v=PxJP16qNCYs"> 10-minute video </a>.

More information on the input syntax as well as details on the the various trajectory
analsyis tools that come with PLUMED are given in: 

- \ref colvarintro tells you about the ways that you can calculate functions of the positions of the atoms.
- \ref Analysis tells you about the various forms of analysis you can run on trajectories using PLUMED.
- \ref Bias tells you about the methods that you can use to bias molecular dynamics simulations with PLUMED.

PLUMED can be used in one of two ways.
First, it can be incorporated into an MD code and used to analyse or bias a molecular dynamics run on the fly.
Notice that 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 2 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/).

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 standalone tool for postprocessing the results from molecular dynamics 
or enhanced sampling calculations.

\page Changelog Change Log

Here you can find a history of changes across different PLUMED versions.
We mostly add new features without breaking exising 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@

*/