user-doc: small changes

[makedoc]

user-doc/Colvar.txt

@@ -10,7 +10,7 @@ implemented in PLUMED - there values can be monitored using \ref PRINT, \ref Fun
 or they can be analyzed or biased using the \ref Analysis and \ref Bias "Biasing" methods implemented in PLUMED.
 Before doing any of these things however we first have to tell PLUMED how to calculate them.
 
-The simplest collective variables that are implemented in PLUMED 2 take in a
+The simplest collective variables that are implemented in PLUMED take in a
 set of atomic positions and output one or multiple scalar CV values.  Information on these variables is given on the page entitled 
 \ref Colvar while information as to how sets of atoms can be selected
 can be found in the pages on \ref Group.  Please be aware that PLUMED contains implementations of many other collective variables 
@@ -34,7 +34,7 @@ implement all these collective variables without implementing having an unmanigi
 
 \page Colvar CV Documentation
 
-The following list contains descriptions of a number of the colvars that are currently implemented in PLUMED 2.
+The following list contains descriptions of a number of the colvars that are currently implemented in PLUMED.
 
 @COLVAR@
 

user-doc/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.
+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.
 PLUMED can also work as a standalone tool to perform analysis on trajectories saved in most of the
 existing formats.
-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>.
 
 To follow the development of PLUMED 2, you can look at the detailed \ref Changelog.
 
+To install PLUMED, see this page: \ref Installation
+
 \ref tutorials are available to introduce in a more practical way basic as well as more
 advanced features of PLUMED.
- 
-To install PLUMED 2, see this page: \ref Installation
 
+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 .
+ 
 \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@
 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),
@@ -38,7 +37,7 @@ please do not print it!
 
 \section qintro A quick introduction
 
-To run PLUMED 2 you need to provide one input file.  In this file you specify what it
+To run PLUMED 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
@@ -56,7 +55,7 @@ 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:
+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

user-doc/Syntax.txt

 /**
 \page Syntax Getting started 
 
-To run PLUMED 2 you need to provide one input file.  In this file you specify what it
+To run PLUMED 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