Added comment on plumed 1.3->2.0 syntax

[makedoc]

closes #147

user-doc/Intro.txt

@@ -18,7 +18,8 @@ An experimental PDF copy of this manual can be found
 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)
+A short tutorial explaining why it is a good idea to move from PLUMED 1 to PLUMED 2
+and how to do it in practice is also available (see \ref moving).
 
 To install PLUMED 2, see this page: \ref Installation
 

user-doc/tutorials/moving.txt

 /**
-\page moving Moving from Plumed 1 to Plumed 2
+\page moving Moving from PLUMED 1 to PLUMED 2
 
-Syntax in PLUMED 2 has been completely redesigned. The main difference is that
+Syntax in PLUMED 2 has been completely redesigned based on our experience
+using PLUMED 1, hopefully makeing it clearer, more flexible, and less error prone.
+The main difference is that
 whereas in PLUMED 1 lines could be inserted in any order, 
 in PLUMED 2 the order of the lines matters. This is due to a major change in 
 the internal architecture of PLUMED. In version 2, commands (or "actions") are
@@ -12,9 +14,52 @@ later. More information can be found in the Section about \ref Syntax.
 Another very important change is in the way groups are used, discussed below.
 Finally, many features appear under a different name in the new version.
 
+\section moving-Syntax New syntax
+
+We know that changing the input syntax requires a lot of work from the user
+side to update their input files. However, we believe that the new syntax is
+easier to read and that it allows for more flexibility.
+As an example, something that in PLUMED 1.3 was:
+\verbatim
+HILLS HEIGHT 0.4 W_STRIDE 600
+WELLTEMPERED SIMTEMP 300  BIASFACTOR 15
+RGYR LIST <all>
+all->
+1   5  6  7   9  11  15  16  17 19
+all<-
+TORSION LIST 5 7 9 15 SIGMA  0.1
+TORSION LIST 7 9 15 17
+PRINT W_STRIDE 100
+\endverbatim
+in PLUMED 2.x becomes:
+\verbatim
+all:  GROUP     ATOMS=1,5,6,7,9,11,15,16,17,19
+rg:   GYRATION  ATOMS=all
+t1:   TORSION ATOMS=5,7,9,15
+METAD ...
+  LABEL=meta
+  ARG=t1 SIGMA=0.1 HEIGHT=0.4 PACE=600
+  BIASFACTOR=15 TEMP=300
+... METAD
+t2:   TORSION ATOMS=7,9,15,17
+PRINT ARG=t1,t2,meta.bias  STRIDE=100   FILE=COLVAR
+\endverbatim
+Giving all quantities an explicit name makes the input easier to interpret.
+Additionally, all the parameters related to \ref METAD are placed on a single line
+(actually, this is done here exploiting continuation lines).
+Also notice that one can customize the name of the `COLVAR` file.
+By specifying to \ref PRINT which collective variables should be printed,
+one can easily decide what to print exactly and using which stride.
+By repeating the \ref PRINT line one can also monitor very expensive variables
+with a larger stride, just putting the result on a separate file.
+
+You might have noticed that ideas that were very difficult to implement in PLUMED 1.3
+now become immediately available. As an example, one can now apply
+concurrently several \ref METAD potentials \cite gil2015enhanced .
+
 \section moving-Groups Groups
 
-In Plumed 1 groups (lists) were used for two tasks:
+In PLUMED 1 groups (lists) were used for two tasks:
 - To provide centers of masses to collective variables such as distances, angles, etc. This is 
   now done by defining virtual atoms using either \ref CENTER or \ref COM
 - To provide lists of atoms to collective variables such as coordination, gyration radius, etc.
@@ -24,11 +69,40 @@ If you would still like to use groups you can use the \ref GROUP commands.  When
 for a \ref GROUP action appears in the input it is replaced by the list of atoms that were 
 specified in the \ref GROUP.
 
+A restraint on the distance between centers of mass in PLUMED 1 was something like:
+\verbatim
+DISTANCE LIST <g1> <g2>
+g1->
+17 20 22 30
+g1<-
+g2->
+LOOP 37 40
+g2<-
+UMBRELLA CV 1 KAPPA 200 AT 1.0
+PRINT W_STRIDE 100
+\endverbatim
+The same in PLUMED 2.x reads:
+\verbatim
+g1: COM ATOMS=17,20,22,30
+g2: COM ATOMS=37-40
+d:  DISTANCE ATOMS=g1,g2
+r:  RESTRAINT ARG=d KAPPA=200 AT=1.0
+PRINT STRIDE=100 FILE=COLVAR ARG=d,r.*
+\endverbatim
+
+Notice that virtual atoms are very powerful tools in PLUMED 2. Actually, they can be used
+in any collective variable where normal atoms can be used, just by calling them by name.
+In this example you can also appreciate the advantage of calling collective variables
+by name. It is obvious here that \ref RESTRAINT is acting on distance `d`, whereas in PLUMED 1
+one had to keep track of the number of the collective variables. This was easy for a single collective variable,
+but could become cumbersome for complex input files.
+
+
 \section moving-Directives Directives
 
-What follows is a list of all the documented directives of Plumed 1 together with their 
+What follows is a list of all the documented directives of PLUMED 1 together with their 
 plumed 2 equivalents.  Be aware that the input syntaxes for these directives are not totally 
-equivalent.  You should read the documentation for the Plumed 2 Action.
+equivalent.  You should read the documentation for the PLUMED 2 Action.
 
 <TABLE>
 <TR>