diff --git a/CHANGES/Unreleased.txt b/CHANGES/Unreleased.txt
index fb014aec7514cc938957ef393a3d2662183a1437..ffda919570ae4f84c4578fb0c8de6fb9cb345059 100644
--- a/CHANGES/Unreleased.txt
+++ b/CHANGES/Unreleased.txt
@@ -12,8 +12,8 @@ Changes from version 2.0 which are relevant for users:
enabled or disabled. An internal version of lapack and blas will be used
if these libraries are not installed.
- The command SPHERE has been replaced by \ref UWALLS
-- Labels of quantities calaculated by BIASVALUE have changed from <label>.bias.<argname> to <label>.<argname>_bias, which is more consistent with steered MD
-- Labels of quantities calculated by ABMD have change from <label>.min_<argname> to <label>.<argname>_min, which is more consistent with steered MD
+- Labels of quantities calaculated by BIASVALUE have changed from <i>label</i>.bias.<i>argname</i> to <i>label</i>.<i>argname</i>_bias, which is more consistent with steered MD
+- Labels of quantities calculated by ABMD have change from <i>label</i>.min_<i>argname</i> to <i>label</i>.<i>argname</i>_min, which is more consistent with steered MD
- New actions:
- \ref SPRINT topological collective variables.
- \ref CH3SHIFTS collective variable.
diff --git a/src/analysis/ClassicalMultiDimensionalScaling.cpp b/src/analysis/ClassicalMultiDimensionalScaling.cpp
index c2066a136d32a40229285b34b0b66199503aecaa..27f4dfb81ef1012c33a82e4f6217fce3e9d93851 100644
--- a/src/analysis/ClassicalMultiDimensionalScaling.cpp
+++ b/src/analysis/ClassicalMultiDimensionalScaling.cpp
@@ -79,7 +79,7 @@ D_{ij}^2 = \sum_{\alpha} (X^i_\alpha - X^j_\alpha)^2 = \sum_\alpha (X^i_\alpha)^
\f]
We can use this expression and matrix algebra to calculate multiple distances at once. For instance if we have three points,
-$\mathbf{X}$, we can write distances between them as:
+\f$\mathbf{X}\f$, we can write distances between them as:
\f{eqnarray*}{
D^2(\mathbf{X}) &=& \left[ \begin{array}{ccc}
diff --git a/src/colvar/RMSD.cpp b/src/colvar/RMSD.cpp
index a69a1d4c349de5dffa13abdf263e64efe2c27ec0..e05aa68c44513da358442c88705d74bca955d0e6 100644
--- a/src/colvar/RMSD.cpp
+++ b/src/colvar/RMSD.cpp
@@ -99,8 +99,7 @@ Here we discuss the switch we implemented so far.
you are working with natural units. If you are working with natural units then the coordinates
should be in your natural length unit. For more details on the PDB file format visit http://www.wwpdb.org/docs.html
.
- - If you use TYPE=OPTIMAL you just the root mean square deviation after reset of the geometric center
- and performing an optimal alignment that reads:
+ - If you use TYPE=OPTIMAL you just the root mean square deviation after reset of the geometric center and performing an optimal alignment that reads:
\f[
d(X,X_r) = \sqrt{ \sum_i \sum_\alpha^{x,y,z} \frac{w_i}{\sum_j w_j}[ X_{i,\alpha}-com_\alpha(X)- \sum_\beta M(X,X',w')_{\alpha,\beta}({X'}_{i,\beta}-com_\beta(X')) ]^2 }
\f]
diff --git a/user-doc/Colvar.txt b/user-doc/Colvar.txt
index e8fe24bb8818f364e488c08b5c3545a591ca69b2..4a4987085ad656d3620f800ce8af6b19d9680105 100644
--- a/user-doc/Colvar.txt
+++ b/user-doc/Colvar.txt
@@ -15,7 +15,7 @@ set of atomic positions and output one or multiple scalar CV values. Informatio
\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
but that the input for these variables may be less transparent when it is first encourntered.
-In particular, the page on \dists describes the various ways that you can calculate the distance from a particular reference
+In particular, the page on \ref dists describes the various ways that you can calculate the distance from a particular reference
configuration. So you will find instructions on how to calculate the RMSD distance from the folded state of a protein here.
Meanwhile, the page on \ref Function describes the various functions of collective variables that can be used in the
code. This is a very powerful feature of PLUMED as you can use the \ref Function commands to calculate any function or
diff --git a/user-doc/Group.txt b/user-doc/Group.txt
index c64dcb8cdcb19fb5b471a8c8d6e62582b22f5b26..978613bde646f7b62e8c56cc1e02e513abe28e68 100644
--- a/user-doc/Group.txt
+++ b/user-doc/Group.txt
@@ -38,17 +38,17 @@ following special groups are currently available in PLUMED:
<table align=center frame=void width=95%% cellpadding=5%%>
<tr> <td width=10%> <b> Symbol </b> </td> <td> <b> Topology type </b> </td> <td> <b> Despription </b> </td> </tr>
-<tr> <td> \@phi-# </td> <td> protein </td> <td>
-The torsional angle defined by the C, CA, N and C atoms of the protein backbone in the #th residue. See http://en.wikipedia.org/wiki/Ramachandran_plot
+<tr> <td> \@phi-\# </td> <td> protein </td> <td>
+The torsional angle defined by the C, CA, N and C atoms of the protein backbone in the \#th residue. See http://en.wikipedia.org/wiki/Ramachandran_plot
</td> </tr>
-<tr> <td> \@psi-# </td> <td> protein </td> <td>
-The torsional angle defined by the N, C, CA and N atoms of the protein backbone in the #th residue. See http://en.wikipedia.org/wiki/Ramachandran_plot
+<tr> <td> \@psi-\# </td> <td> protein </td> <td>
+The torsional angle defined by the N, C, CA and N atoms of the protein backbone in the \#th residue. See http://en.wikipedia.org/wiki/Ramachandran_plot
</td> </tr>
-<tr> <td> \@omega-# </td> <td> protein </td> <td>
-The torsional angle defined by the CA, N, C and CA atoms of the protein backbone in the #th residue. See http://en.wikipedia.org/wiki/Ramachandran_plot
+<tr> <td> \@omega-\# </td> <td> protein </td> <td>
+The torsional angle defined by the CA, N, C and CA atoms of the protein backbone in the \#th residue. See http://en.wikipedia.org/wiki/Ramachandran_plot
</td> </tr>
-<tr> <td> \@chi1-# </td> <td> protein </td> <td>
-The first torsional angle of the sidechain of the #th residue. Be aware that this angle is not defined for GLY or ALA residues.
+<tr> <td> \@chi1-\# </td> <td> protein </td> <td>
+The first torsional angle of the sidechain of the \#th residue. Be aware that this angle is not defined for GLY or ALA residues.
See http://en.wikipedia.org/wiki/Ramachandran_plot
</td> </tr>
</table>
diff --git a/user-doc/Syntax.txt b/user-doc/Syntax.txt
index 5de6adfafa3b89905281c0b2a891c2db991e0e8b..75a40541c073deb0bce81c0c503a6077a53c6916 100644
--- a/user-doc/Syntax.txt
+++ b/user-doc/Syntax.txt
@@ -39,7 +39,7 @@ PRINT ARG=d1 FILE=colvar STRIDE=10
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,
+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