diff --git a/user-doc/Colvar.txt b/user-doc/Colvar.txt
index f5628aef4edddb0fc730efbeb0c9bf47f1e07da1..c92e004b749dc81ecb36335e69aed1280b5be990 100644
--- a/user-doc/Colvar.txt
+++ b/user-doc/Colvar.txt
@@ -10,93 +10,6 @@ implemented in PLUMED - they're values can be monitored using \ref PRINT, \ref F
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 inform PLUMED how to calculate them.
-\section atomSpecs Specifying Atoms
-
-The vast majority of the CVs implemented in PLUMED are calculated from a list of atom positions. Within PLUMED
-atoms are always specified according to their numerical indices in the molecular dynamics input file. This can
-be done either using a comma separated list of numbers or, if a long list atom of contiguous atoms is required,
-by using the shortcut 10-100, which specifies all the atom indexes between 10 and 100 (including 10 and 100). So for example:
-
-\verbatim
-TORSION ATOMS=1,2,3,4
-\endverbatim
-
-could also be specified using:
-
-\verbatim
-TORIONS ATOMS=1-4
-\endverbatim
-
-Ranges of atom can also be defined with a stride. For example:
-
-\verbatim
-COM ATOMS=1,11,21,31,41,51
-\endverbatim
-
-could also be specified using:
-
-\verbatim
-COM ATOMS=1-51:10
-\endverbatim
-
-One can also obtain a list of decreasing indexes e.g. with
-
-\verbatim
-GROUP ATOMS=51-1:-10
-# same as GROUP ATOMS=51,41,31,21,11,1
-\endverbatim
-
-Notice that most expressions are invariant with respect to a change in the order of the atoms,
-but some of them depend on that order. E.g., with \ref WHOLEMOLECULES it could be useful to
-specify atom lists in a reversed order.
-
-
-
-
-In addition, for certain colvars, pdb files can be read in using the following keywords:
-
-@TOPOLOGY@
-
-The read in pdb files are used by PLUMED to define things like residues, the backbone atoms and so on. These can then be
-used within the input to colvars to make inputting the lists of atoms involved more straightforward. Documentation for
-how these shortcuts can be used can be found in the documentation for the various CVs.
-
-Lastly, if you have a list of colvar that is particularly laborious to write out that you need to use multiple times in the
-input you can create a static group of atoms and then use the label of the group to specify the correpsonding list of
-atoms in your various colvars. For more details see \subpage GROUP.
-
-\section vatoms Virtual Atoms
-
-Sometimes, when calculating a colvar, you may not want to use the positions of a number of atoms directly. Instead
- you may wish to use the position of a virtual atom whose position is generated based on the positions of a collection
-of other atoms. For example you might want to use the center of mass of a group of atoms. Plumed has a number of routines
-for calculating the positions of these virtual atoms from lists of atoms:
-
-@VATOM@
-
-To specify to a colvar that you want to use the position of a virtual atom to calculate a colvar rather than one of the atoms
-in your system you simply use the label for your virtual atom in place of the usual numerical index. Virtual
-atoms and normal atoms can be mixed together in the input to colvars as shown below:
-
-\verbatim
-COM ATOMS=1,10 LABEL=com1
-DISTANCE ATOMS=11,com1
-\endverbatim
-
-If you don't want to calculate CVs from the virtual atom. That is to say you just want to monitor the position of a virtual atom
-(or any set of atoms) over the course of your trajectory you can do this using \ref DUMPATOMS.
-
-\section mols Molecules
-
-PLUMED is designed so that for the majority of the CVs implemented the periodic boundary conditions are treated
-in the same manner as they would be treated in the host code. In some codes this can be problematic when the colvars
-you are using involve some property of a molecule. These codes allow the atoms in the molecules to become separated by
-periodic boundaries, a fact which PLUMED could only deal with were the topology passed from the MD code to PLUMED. Making this
-work would involve a lot laborious programming and goes against our original aim of having a general patch that can be implemented
-in a wide variety of MD codes. Consequentially, we have implemented a more pragmatic solution to this probem - the user specifies
-in input any molecules (or parts of molecules) that must be kept in tact throughout the simulation run. In PLUMED 1 this was done
-using the ALIGN_ATOMS keyword. In PLUMED 2 the same effect can be acchieved using the \subpage WHOLEMOLECULES command.
-
\section cvavail CV Documentation
The following list contains descriptions of a number of the colvars that are currently implemented in PLUMED 2.
diff --git a/user-doc/Doxyfile b/user-doc/Doxyfile
index 1b99f3b7a0e9e32574d825015c266ddb2f232d57..6c5ce37d73b1bac1073a95dc2decb8b3bc13080b 100644
--- a/user-doc/Doxyfile
+++ b/user-doc/Doxyfile
@@ -738,6 +738,7 @@ INPUT = IntroPP.txt \
AnalysisPP.txt \
ColvarPP.txt \
FunctionsPP.txt \
+ GroupPP.txt \
InstallationPP.txt \
GlossaryPP.txt \
TutorialsPP.txt \
diff --git a/user-doc/Group.txt b/user-doc/Group.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3dc061a3b05d2da8ecec862c31060041c1cce2ae
--- /dev/null
+++ b/user-doc/Group.txt
@@ -0,0 +1,67 @@
+/**
+
+\page Group Groups and Virtual Atoms
+
+\section atomSpecs Specifying Atoms
+
+The vast majority of the CVs implemented in PLUMED are calculated from a list of atom positions. Within PLUMED
+atoms are always specified according to their numerical indices in the molecular dynamics input file.
+
+In PLUMED lists of atoms can be either provided directly inside the definition of each collective variable, or
+predefined as \ref GROUP that can be reused multiple times. Atoms' list can be defined as:
+
+- comma separated list of numbers (GROUP ATOMS=10,11,15,20 LABEL=g1)
+- atoms ranges (i.e. GROUP ATOMS=10-100 LABEL=g2)
+- atoms ranges with a stride (i.e. GROUP ATOMS=10-100:10 LABEL=g3)
+- atoms ranges with a negative stride (i.e. GROUP ATOMS=100-10:-10 LABEL=g4)
+- all the above methods together (i.e. GROUP ATOMS=1,2,10-20,40-60:5,100-70:-2 LABEL=g5).
+
+Note that some collective variable can only accept a fixed number of atoms, for example a \ref DISTANCE is calculated
+using two atoms only.
+
+Notice that most expressions are invariant with respect to a change in the order of the atoms,
+but some of them depend on that order. E.g., with \ref WHOLEMOLECULES it could be useful to
+specify atom lists in a reversed order.
+
+In addition, for certain colvars, pdb files can be read in using the following keywords:
+
+@TOPOLOGY@
+
+The read in pdb files are used by PLUMED to define things like residues, the backbone atoms and so on. These can then be
+used within the input to colvars to make inputting the lists of atoms involved more straightforward. Documentation for
+how these shortcuts can be used can be found in the documentation for the various CVs.
+
+\section vatoms Virtual Atoms
+
+Sometimes, when calculating a colvar, you may not want to use the positions of a number of atoms directly. Instead
+ you may wish to use the position of a virtual atom whose position is generated based on the positions of a collection
+of other atoms. For example you might want to use the center of mass of a group of atoms. Plumed has a number of routines
+for calculating the positions of these virtual atoms from lists of atoms:
+
+@VATOM@
+
+To specify to a colvar that you want to use the position of a virtual atom to calculate a colvar rather than one of the atoms
+in your system you simply use the label for your virtual atom in place of the usual numerical index. Virtual
+atoms and normal atoms can be mixed together in the input to colvars as shown below:
+
+\verbatim
+COM ATOMS=1,10 LABEL=com1
+DISTANCE ATOMS=11,com1
+\endverbatim
+
+If you don't want to calculate CVs from the virtual atom. That is to say you just want to monitor the position of a virtual atom
+(or any set of atoms) over the course of your trajectory you can do this using \ref DUMPATOMS.
+
+\section mols Molecules
+
+PLUMED is designed so that for the majority of the CVs implemented the periodic boundary conditions are treated
+in the same manner as they would be treated in the host code. In some codes this can be problematic when the colvars
+you are using involve some property of a molecule. These codes allow the atoms in the molecules to become separated by
+periodic boundaries, a fact which PLUMED could only deal with were the topology passed from the MD code to PLUMED. Making this
+work would involve a lot laborious programming and goes against our original aim of having a general patch that can be implemented
+in a wide variety of MD codes. Consequentially, we have implemented a more pragmatic solution to this probem - the user specifies
+in input any molecules (or parts of molecules) that must be kept in tact throughout the simulation run. In PLUMED 1 this was done
+using the ALIGN_ATOMS keyword. In PLUMED 2 the same effect can be acchieved using the \subpage WHOLEMOLECULES command.
+
+*/
+
diff --git a/user-doc/PlumedLayout.xml b/user-doc/PlumedLayout.xml
index e90c76b313ceaa11bbadb8a0859c26db62acb830..49d7ddcc650111ad6fe36edd0233985c3676ef89 100644
--- a/user-doc/PlumedLayout.xml
+++ b/user-doc/PlumedLayout.xml
@@ -3,8 +3,14 @@
<navindex>
<tab type="mainpage" visible="yes" title=""/>
<tab type="user" visible="no" url="mymodules.html" title="Modules"/>
+ <tab type="user" visible="yes" url="_installation.html" title="Installation"/>
+ <tab type="user" visible="yes" url="tutorials.html" title="Tutorials"/>
+ <tab type="user" visible="yes" url="_group.html" title="Groups and Atoms"/>
+ <tab type="user" visible="yes" url="_colvar.html" title="Collective Variables"/>
+ <tab type="user" visible="yes" url="_function.html" title="Functions"/>
+ <tab type="user" visible="yes" url="_analysis.html" title="Analysis"/>
+ <tab type="user" visible="yes" url="_bias.html" title="Bias"/>
<tab type="user" visible="yes" url="glossary.html" title="Glossary"/>
- <tab type="user" visible="yes" url="tutorials.html" title="How-tos"/>
<tab type="pages" visible="no" title="" intro=""/>
<tab type="modules" visible="yes" title="" intro=""/>
<tab type="namespaces" visible="yes" title="">
diff --git a/user-doc/Tutorials.txt b/user-doc/Tutorials.txt
index a3d30f4353039fdc5a31cc32e2b25f6fc0acaaa9..8360e59a8ae8fe24ce492f02b295442a4144ba35 100644
--- a/user-doc/Tutorials.txt
+++ b/user-doc/Tutorials.txt
@@ -1,6 +1,6 @@
/**
-@page tutorials How-tos
+@page tutorials Tutorials
The following pages describe how to perform a variety of tasks using PLUMED 2
diff --git a/user-doc/extract b/user-doc/extract
index 5027554330c7b7efeda582d8a342c35e41582229..a284e5be89385b752248d6d426df36ae826737db 100755
--- a/user-doc/extract
+++ b/user-doc/extract
@@ -213,7 +213,7 @@ do
fi
done
-for file in Bias Colvar Functions Installation Intro Analysis Glossary Tutorials Modules Regex
+for file in Bias Colvar Functions Group Installation Intro Analysis Glossary Tutorials Modules Regex
do
cat $file.txt |