Some fixes in doc

(backported from 2.1)

user-doc/Analysis.txt

@@ -2,8 +2,9 @@
 
 \page Analysis Analysis
 
-Once you have calculated a number of collective variables PLUMED allows you to either analyse
-your trajectory.  The list of available on-the-fly analysis tools contains:
+PLUMED can be used to analyse trajectories either on the fly during an MD run or via
+postprocessing a trajectory using \ref driver.  The following is a list of the various
+methods for analysing trajectories contained in PLUMED.
 
 @ANALYSIS@
 

user-doc/Bias.txt

@@ -2,13 +2,12 @@
 
 \page Bias Bias
 
-Once you have calculated a number of collective variables PLUMED allows you to
-run a number of enhanced sampling algorithms.
-The list of available enhanced sampling algorithms contains: 
+PLUMED allows you to run a number of enhanced sampling algorithms.
+The list of enhanced sampling algorithms contained in PLUMED is as follows: 
 
 @BIAS@
 
-Methods, such as \ref METAD, that introduce a history dependent bias can be restarted 
+Methods, such as \ref METAD, that work by introducing a history dependent bias can be restarted 
 using the \subpage RESTART keyword
 
 You can also use PLUMED in conjunction with VMD's interactive MD module by taking

user-doc/Intro.txt

@@ -3,14 +3,15 @@
 
 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 was highly successful and had over 1000 users.  PLUMED 2 \cite plumed2 constitues an 
+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 know the difference between PLUMED 1 and PLUMED 2, and to
-follow the development of PLUMED 2, you can checkout the detailed changelog:
+To understand the difference between PLUMED 1 and PLUMED 2, and to
+follow the development of PLUMED 2, you can look at the detailed changelog:
 - Changes for \ref CHANGES-2-0
 
 A short tutorial explaining how to move from PLUMED 1 to PLUMED 2 is also available (see \ref moving)