diff --git a/user-doc/Doxyfile b/user-doc/Doxyfile
index 6c5ce37d73b1bac1073a95dc2decb8b3bc13080b..b9919b5e3f7fa7592e00d4e82344eebfc4b584a2 100644
--- a/user-doc/Doxyfile
+++ b/user-doc/Doxyfile
@@ -737,6 +737,7 @@ INPUT = IntroPP.txt \
BiasPP.txt \
AnalysisPP.txt \
ColvarPP.txt \
+ SyntaxPP.txt \
FunctionsPP.txt \
GroupPP.txt \
InstallationPP.txt \
diff --git a/user-doc/Intro.txt b/user-doc/Intro.txt
index 9c442514bc0ec767784746e6dd9fcacc5b27be82..5154a4ff7579e404b52dd18223dba059cee1f3a2 100644
--- a/user-doc/Intro.txt
+++ b/user-doc/Intro.txt
@@ -50,160 +50,8 @@ The following is a list of the various standalone tools that PLUMED contains.
@TOOLS@
-For all these tools and to use PLUMED as a plugin in an MD calculation you will need an input file. Within
-this input file every line is an instruction for PLUMED to perform some particular action. This could be
- the calculation of a colvar, an occasional analysis of the trajectory or a biassing of the dynamics. The first
-word in these lines specify what particular action is to be performed. This is then followed by a number of keywords
-which provide PLUMED with more details as to how the action is to be performed. These keywords are either single words
-(in which they tell PLUMED to do the calculation in a particular way - for example NOPBC tells PLUMED to not use the periodic
-bounadry conditions when calculating a particular colvar) or they can be words followed by an equals sign and a comma separated
-list - WITH NO SPACES - of numbers or characters (so for example ATOMS=1,2,3,4 tells PLUMED to use atom numbers 1,2,3 and 4 in
-the calculation of a particular colvar). Space separated lists can be used instead of commma separated list if the entire list
-is enclosed in curly braces (e.g. ATOMS={1 2 3 4}).
-
-The most important of these keywords is the label keyword as it is only by using these labels that we can pass data
-from one action to another. As an example if you do:
+For all these tools and to use PLUMED as a plugin in an MD calculation you will need an input file.
-\verbatim
-DISTANCE ATOMS=1,2
-\endverbatim
-(see \ref DISTANCE)
-
-Then PLUMED will do nothing other than read in your input file. In contrast if you do:
-
-\verbatim
-DISTANCE ATOMS=1,2 LABEL=d1
-PRINT ARG=d1 FILE=colvar STRIDE=10
-\endverbatim
-(see \ref PRINT)
-
-then PLUMED will print out the value of the distance between atoms 1 and 2 every 10 steps to the file colvar as you have told
-PLUMED to take the value calculated by the action d1 and to print it. You can use any character string to label your actions
-as long as it does not begin with the symbol @. Strings beginning with @ are used by within PLUMED to reference special,
-code-generated groups of atoms and to give labels to any Actions for which the user does not provide a label in the input.
-
-Notice that if a word followed by a column is added at the beginning of the line (e.g. pippo:), PLUMED automatically
-removes it and adds an equivalent label (LABEL=pippo).
-Thus, a completely equivalent result can be obtained with the following shortcut:
-\verbatim
-d1: DISTANCE ATOMS=1,2
-PRINT ARG=d1 FILE=colvar STRIDE=10
-\endverbatim
-
-Also notice that all the actions can be labeled, and that many actions besides normal collective variables can define
-one or more value, which can be then referred using the corresponding label.
-
-Actions can be referred also with POSIX regular expressions (see \ref Regex). For this you need to compile PLUMED with the appropriate flag.
-
-\section Units A note on units
-By default the PLUMED inputs and outputs quantities in the following units:
-
-- Energy - kJ/mol
-- Length - nanometers
-- Time - picoseconds
-
-Unlike PLUMED 1 the units used are independent of the MD engine you are using. If you want to change these units you can do this using the
-\ref UNITS keyword.
-
-Those are the essentials but there are a few other tricks that we didn't know where else to put in the manual so we stuck them here.
-
-\section comments Comments
-
-If you are an organised sort of person who likes to remember what the hell you were trying to do when you ran a
-particular simulation you might find it useful to put comments in your input file. In PLUMED you can do this as
-comments can be added using a # sign. On any given line everything after the # sign is ignored so
-erm... yes add lines of comments or trailing comments to your hearts content as shown below (using Shakespeare is optional):
-
-\verbatim
-# This is the distance between two atoms:
-DISTANCE ATOM=1,2 LABEL=d1
-UPPER_WALLS ARG=d1 AT=3.0 KAPPA=3.0 LABEL=Snout # In this same interlude it doth befall. That I, one Snout by name, present a wall.
-\endverbatim
-(see \ref DISTANCE and \ref UPPER_WALLS)
-
-An alternative to including comments in this way is to use line starting ENDPLUMED. Everything in the PLUMED input after this
-keyword will be ignored.
-
-\section ContinuationLines Continuation lines
-
-If your input lines get very long then editing them using vi and other such text editors becomes a massive pain in the arse.
-We at PLUMED are aware of this fact and thus have provided a way of doing line continuations so as to make your life that much
-easier - aren't we kind? Well no not really, we have to use this code too. Anyway, you can do continuations by using the "..." syntax
-as this makes this:
-
-\verbatim
-DISTANCES ATOMS1=1,300 ATOMS2=1,400 ATOMS3=1,500
-\endverbatim
-(see \ref DISTANCES)
-
-equivalent to this:
-
-\verbatim
-DISTANCES ...
-# we can also insert comments here
- ATOMS1=1,300
-# multiple kewords per line are allowed
- ATOMS2=1,400 ATOMS3=1,500
-#empty lines are also allowed
-
-... DISTANCES
-\endverbatim
-
-\section includes Including other files in the PLUMED input
-
-If, for some reason, you want to spread your PLUMED input over a number of files you can use \ref INCLUDE as shown below:
-
-\verbatim
-INCLUDE FILE=filename
-\endverbatim
-
-So, for example, a single "plumed.dat" file:
-
-\verbatim
-DISTANCE ATOMS=0,1 LABEL=dist
-RESTRAINT ARG=dist
-\endverbatim
-(see \ref DISTANCE and \ref RESTRAINT)
-
-could be split up into two files as shown below:
-
-\verbatim
-DISTANCE ATOMS=0,1 LABEL=dist
-INCLUDE FILE=toBeIncluded.dat
-\endverbatim
-plus a "toBeIncluded.dat" file
-\verbatim
-RESTRAINT ARG=dist
-\endverbatim
-
-However, when you do this it is important to recognise that \ref INCLUDE is a real directive that is only resolved
-after all the \ref comments have been stripped and the \ref ContinuationLines have been unrolled. This means it
-is not possible to do things like:
-
-\verbatim
-# this is wrong:
-DISTANCE INCLUDE FILE=options.dat
-RESTRAINT ARG=dist
-\endverbatim
-
-\section load Loading shared libraries
-
-You can introduce new functionality into PLUMED by placing it directly into the src directory and recompiling the
-PLUMED libraries. Alternatively, if you want to keep your code independent from the rest of PLUMED (perhaps
-so you can release it independely - we won't be offended), then you can create your own dynamic library. To use this
-in conjuction with PLUMED you can then load it at runtime by using the \ref LOAD keyword as shown below:
-
-\verbatim
-LOAD FILE=library.so
-\endverbatim
-
-N.B. If your system uses a different suffix for dynamic libraries (e.g. macs use .dylib) then PLUMED will try to
-automatically adjust the suffix accordingly.
-
-\section degub Debugging the code
-
-The \ref DEBUG action provides some functionality for debugging the code that may be useful if you are doing
-very intensive development of the code of if you are running on a computer with a strange architecture.
*/
diff --git a/user-doc/Syntax.txt b/user-doc/Syntax.txt
new file mode 100644
index 0000000000000000000000000000000000000000..69777ac15ef269331b71ada2d70690b8b041460f
--- /dev/null
+++ b/user-doc/Syntax.txt
@@ -0,0 +1,175 @@
+/**
+\page Syntax Syntax
+
+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 Colvar tells you about the functions of the positions atoms that PLUMED can calculate.
+- \ref Function tells you about the functions of collective variables that PLUMED can calculate.
+- \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.
+
+
+Within this input file every line is an instruction for PLUMED to perform some particular action. This could be
+ the calculation of a colvar, an occasional analysis of the trajectory or a biassing of the dynamics. The first
+word in these lines specify what particular action is to be performed. This is then followed by a number of keywords
+which provide PLUMED with more details as to how the action is to be performed. These keywords are either single words
+(in which they tell PLUMED to do the calculation in a particular way - for example NOPBC tells PLUMED to not use the periodic
+bounadry conditions when calculating a particular colvar) or they can be words followed by an equals sign and a comma separated
+list - WITH NO SPACES - of numbers or characters (so for example ATOMS=1,2,3,4 tells PLUMED to use atom numbers 1,2,3 and 4 in
+the calculation of a particular colvar). Space separated lists can be used instead of commma separated list if the entire list
+is enclosed in curly braces (e.g. ATOMS={1 2 3 4}).
+
+The most important of these keywords is the label keyword as it is only by using these labels that we can pass data
+from one action to another. As an example if you do:
+
+\verbatim
+DISTANCE ATOMS=1,2
+\endverbatim
+(see \ref DISTANCE)
+
+Then PLUMED will do nothing other than read in your input file. In contrast if you do:
+
+\verbatim
+DISTANCE ATOMS=1,2 LABEL=d1
+PRINT ARG=d1 FILE=colvar STRIDE=10
+\endverbatim
+(see \ref PRINT)
+
+then PLUMED will print out the value of the distance between atoms 1 and 2 every 10 steps to the file colvar as you have told
+PLUMED to take the value calculated by the action d1 and to print it. You can use any character string to label your actions
+as long as it does not begin with the symbol @. Strings beginning with @ are used by within PLUMED to reference special,
+code-generated groups of atoms and to give labels to any Actions for which the user does not provide a label in the input.
+
+Notice that if a word followed by a column is added at the beginning of the line (e.g. pippo:), PLUMED automatically
+removes it and adds an equivalent label (LABEL=pippo).
+Thus, a completely equivalent result can be obtained with the following shortcut:
+\verbatim
+d1: DISTANCE ATOMS=1,2
+PRINT ARG=d1 FILE=colvar STRIDE=10
+\endverbatim
+
+Also notice that all the actions can be labeled, and that many actions besides normal collective variables can define
+one or more value, which can be then referred using the corresponding label.
+
+Actions can be referred also with POSIX regular expressions (see \ref Regex). For this you need to compile PLUMED with the appropriate flag.
+
+\section Units A note on units
+By default the PLUMED inputs and outputs quantities in the following units:
+
+- Energy - kJ/mol
+- Length - nanometers
+- Time - picoseconds
+
+Unlike PLUMED 1 the units used are independent of the MD engine you are using. If you want to change these units you can do this using the
+\ref UNITS keyword.
+
+Those are the essentials but there are a few other tricks that we didn't know where else to put in the manual so we stuck them here.
+
+\section comments Comments
+
+If you are an organised sort of person who likes to remember what the hell you were trying to do when you ran a
+particular simulation you might find it useful to put comments in your input file. In PLUMED you can do this as
+comments can be added using a # sign. On any given line everything after the # sign is ignored so
+erm... yes add lines of comments or trailing comments to your hearts content as shown below (using Shakespeare is optional):
+
+\verbatim
+# This is the distance between two atoms:
+DISTANCE ATOM=1,2 LABEL=d1
+UPPER_WALLS ARG=d1 AT=3.0 KAPPA=3.0 LABEL=Snout # In this same interlude it doth befall. That I, one Snout by name, present a wall.
+\endverbatim
+(see \ref DISTANCE and \ref UPPER_WALLS)
+
+An alternative to including comments in this way is to use line starting ENDPLUMED. Everything in the PLUMED input after this
+keyword will be ignored.
+
+\section ContinuationLines Continuation lines
+
+If your input lines get very long then editing them using vi and other such text editors becomes a massive pain in the arse.
+We at PLUMED are aware of this fact and thus have provided a way of doing line continuations so as to make your life that much
+easier - aren't we kind? Well no not really, we have to use this code too. Anyway, you can do continuations by using the "..." syntax
+as this makes this:
+
+\verbatim
+DISTANCES ATOMS1=1,300 ATOMS2=1,400 ATOMS3=1,500
+\endverbatim
+(see \ref DISTANCES)
+
+equivalent to this:
+
+\verbatim
+DISTANCES ...
+# we can also insert comments here
+ ATOMS1=1,300
+# multiple kewords per line are allowed
+ ATOMS2=1,400 ATOMS3=1,500
+#empty lines are also allowed
+
+... DISTANCES
+\endverbatim
+
+\section includes Including other files in the PLUMED input
+
+If, for some reason, you want to spread your PLUMED input over a number of files you can use \ref INCLUDE as shown below:
+
+\verbatim
+INCLUDE FILE=filename
+\endverbatim
+
+So, for example, a single "plumed.dat" file:
+
+\verbatim
+DISTANCE ATOMS=0,1 LABEL=dist
+RESTRAINT ARG=dist
+\endverbatim
+(see \ref DISTANCE and \ref RESTRAINT)
+
+could be split up into two files as shown below:
+
+\verbatim
+DISTANCE ATOMS=0,1 LABEL=dist
+INCLUDE FILE=toBeIncluded.dat
+\endverbatim
+plus a "toBeIncluded.dat" file
+\verbatim
+RESTRAINT ARG=dist
+\endverbatim
+
+However, when you do this it is important to recognise that \ref INCLUDE is a real directive that is only resolved
+after all the \ref comments have been stripped and the \ref ContinuationLines have been unrolled. This means it
+is not possible to do things like:
+
+\verbatim
+# this is wrong:
+DISTANCE INCLUDE FILE=options.dat
+RESTRAINT ARG=dist
+\endverbatim
+
+\section load Loading shared libraries
+
+You can introduce new functionality into PLUMED by placing it directly into the src directory and recompiling the
+PLUMED libraries. Alternatively, if you want to keep your code independent from the rest of PLUMED (perhaps
+so you can release it independely - we won't be offended), then you can create your own dynamic library. To use this
+in conjuction with PLUMED you can then load it at runtime by using the \ref LOAD keyword as shown below:
+
+\verbatim
+LOAD FILE=library.so
+\endverbatim
+
+N.B. If your system uses a different suffix for dynamic libraries (e.g. macs use .dylib) then PLUMED will try to
+automatically adjust the suffix accordingly.
+
+\section degub Debugging the code
+
+The \ref DEBUG action provides some functionality for debugging the code that may be useful if you are doing
+very intensive development of the code of if you are running on a computer with a strange architecture.
+
+*/
+
diff --git a/user-doc/extract b/user-doc/extract
index a284e5be89385b752248d6d426df36ae826737db..7d221b5bfa883a81e6c9c5d32044df7d70b9f61a 100755
--- a/user-doc/extract
+++ b/user-doc/extract
@@ -213,7 +213,7 @@ do
fi
done
-for file in Bias Colvar Functions Group Installation Intro Analysis Glossary Tutorials Modules Regex
+for file in Bias Syntax Colvar Functions Group Installation Intro Analysis Glossary Tutorials Modules Regex
do
cat $file.txt |