diff --git a/src/analysis/Commit.cpp b/src/analysis/Commit.cpp
index 1b7a3ccf6818d99b9b4aa9f37c76bde89f96781f..dab62d8b4c670ff64123ba1e3b374a1a631bcd48 100644
--- a/src/analysis/Commit.cpp
+++ b/src/analysis/Commit.cpp
@@ -33,6 +33,7 @@ namespace analysis {
 Does a committor analysis.
 
 \par Examples
+
 The following input monitors two torsional angles during a simulation,
 defines two basins (A and B) as a function of the two torsions and
 stops the simulation when it falls in one of the two. In the log
diff --git a/src/bias/ABMD.cpp b/src/bias/ABMD.cpp
index 1fdedf3240745c04069d52bb59915cbaa6f723d6..12aa76eb88c6aa8aeef2399b24c0a61f835b0411 100644
--- a/src/bias/ABMD.cpp
+++ b/src/bias/ABMD.cpp
@@ -67,6 +67,7 @@ molecules, the biasing potential does not exert work on the system. \f$\eta(t)\f
 an additional white noise acting on the minimum position of the bias.
 
 \par Examples
+
 The following input sets up two biases, one on the distance between atoms 3 and 5
 and another on the distance between atoms 2 and 4. The two target values are defined
 using TO and the two strength using KAPPA. The total energy of the bias is printed.
diff --git a/src/bias/External.cpp b/src/bias/External.cpp
index 4a1a6befa62b082df32a6fb49ecae17d5066524a..8ff721c0938b2bc1b512cbb6507ffe8f4fa2938a 100644
--- a/src/bias/External.cpp
+++ b/src/bias/External.cpp
@@ -37,6 +37,7 @@ namespace bias {
 Calculate a restraint that is defined on a grid that is read during start up
 
 \par Examples
+
 The following is an input for a calculation with an external potential that is
 defined in the file bias.dat and that acts on the distance between atoms 3 and 5.
 \verbatim
diff --git a/src/bias/LWalls.cpp b/src/bias/LWalls.cpp
index 5f05d124bd2ea9fd3b39a5cccf5a239775b2b4f1..592fce66878b7783e82e765c49a15aac541907a4 100644
--- a/src/bias/LWalls.cpp
+++ b/src/bias/LWalls.cpp
@@ -48,6 +48,7 @@ The expression for the bias due to the wall is given by:
 
 
 \par Examples
+
 The following input tells plumed to add both a lower and an upper walls on the distance
 between atoms 3 and 5 and the distance between atoms 2 and 4. The lower and upper limits
 are defined at different values. The strength of the walls is the same for the four cases.
diff --git a/src/bias/MetaD.cpp b/src/bias/MetaD.cpp
index 4be9a8b3fa11968028f1ce524fbe0456d4448510..b4f09a8936684b699f5aa763896eb4ad2b845042 100644
--- a/src/bias/MetaD.cpp
+++ b/src/bias/MetaD.cpp
@@ -159,6 +159,7 @@ as done e.g. in Ref. \cite gil2015enhanced . This indeed can be obtained by usin
 action multiple times in the same input file.
 
 \par Examples
+
 The following input is for a standard metadynamics calculation using as
 collective variables the distance between atoms 3 and 5
 and the distance between atoms 2 and 4. The value of the CVs and
diff --git a/src/bias/MovingRestraint.cpp b/src/bias/MovingRestraint.cpp
index ae9f1c5fe27c67b29e4616a6dfe7fc71643e10ce..1d8b11dd643d9a0e3f4972990f5a84b004df2464 100644
--- a/src/bias/MovingRestraint.cpp
+++ b/src/bias/MovingRestraint.cpp
@@ -50,6 +50,7 @@ the values of \f$\kappa\f$ and \f$\vec{s}_0\f$ are linearly interpolated.
 Additional material and examples can be also found in the tutorial \ref belfast-5
 
 \par Examples
+
 The following input is dragging the distance between atoms 2 and 4
 from 1 to 2 in the first 1000 steps, then back in the next 1000 steps.
 In the following 500 steps the restraint is progressively switched off.
diff --git a/src/bias/PBMetaD.cpp b/src/bias/PBMetaD.cpp
index 5840eee82b57161888e6037090fa79201679274e..a075ecb40bb89480f73446806c42a92ac6dc852d 100644
--- a/src/bias/PBMetaD.cpp
+++ b/src/bias/PBMetaD.cpp
@@ -137,6 +137,7 @@ boundaries. Note that:
 Multiple walkers  \cite multiplewalkers can also be used, in the MPI implementation only. See below the examples.
 
 \par Examples
+
 The following input is for PBMetaD calculation using as
 collective variables the distance between atoms 3 and 5
 and the distance between atoms 2 and 4. The value of the CVs and
diff --git a/src/bias/Restraint.cpp b/src/bias/Restraint.cpp
index 76a963fefeadcdbc44f053f4b338f62ea3f6ed0f..84e2303b9b09cc5bcf565add7bc7c42c623f808d 100644
--- a/src/bias/Restraint.cpp
+++ b/src/bias/Restraint.cpp
@@ -46,6 +46,7 @@ of arguments to the action.
 Additional material and examples can be also found in the tutorial \ref belfast-4
 
 \par Examples
+
 The following input tells plumed to restrain the distance between atoms 3 and 5
 and the distance between atoms 2 and 4, at different equilibrium
 values, and to print the energy of the restraint
diff --git a/src/bias/UWalls.cpp b/src/bias/UWalls.cpp
index 172f6bdd99b38eaa95db5387c6b95e2c3f45e945..5eb0dd0602d331845243b0b5a3dc7bdb847370e2 100644
--- a/src/bias/UWalls.cpp
+++ b/src/bias/UWalls.cpp
@@ -48,6 +48,7 @@ The expression for the bias due to the wall is given by:
 
 
 \par Examples
+
 The following input tells plumed to add both a lower and an upper walls on the distance
 between atoms 3 and 5 and the distance between atoms 2 and 4. The lower and upper limits
 are defined at different values. The strength of the walls is the same for the four cases.
diff --git a/src/colvar/Cell.cpp b/src/colvar/Cell.cpp
index 266bb0393fda5fe553cff28da77d30e77903e6d5..53d799a39105d31a080a4892113c64cad45c0174 100644
--- a/src/colvar/Cell.cpp
+++ b/src/colvar/Cell.cpp
@@ -35,6 +35,7 @@ namespace colvar {
 Calculate the components of the simulation cell
 
 \par Examples
+
 The following input tells plumed to print the squared modulo of each of the three lattice vectors
 \verbatim
 cell: CELL
diff --git a/src/colvar/DHEnergy.cpp b/src/colvar/DHEnergy.cpp
index 29d03589b2e8ff0b38dbf8f2868bbb30159fb2f7..aaf0a35d65cddd4d767299bf36581a0fdf94c8c1 100644
--- a/src/colvar/DHEnergy.cpp
+++ b/src/colvar/DHEnergy.cpp
@@ -56,6 +56,7 @@ Notice that if there are common atoms between GROUPA and GROUPB their interactio
 
 
 \par Examples
+
 \verbatim
 # this is printing the electrostatic interaction between two groups of atoms
 dh: DHENERGY GROUPA=1-10 GROUPB=11-20 EPSILON=80.0 I=0.1 TEMP=300.0
diff --git a/src/colvar/Dipole.cpp b/src/colvar/Dipole.cpp
index 166dbf68fcaed7df270c4f124620ee7b49616ebc..5f6748db6ab85f1ce60870a79bbe9581dd56c029 100644
--- a/src/colvar/Dipole.cpp
+++ b/src/colvar/Dipole.cpp
@@ -35,6 +35,7 @@ namespace colvar {
 Calculate the dipole moment for a group of atoms.
 
 \par Examples
+
 The following tells plumed to calculate the dipole of the group of atoms containing
 the atoms from 1-10 and print it every 5 steps
 \verbatim
diff --git a/src/colvar/Energy.cpp b/src/colvar/Energy.cpp
index 891285e146039c9377d09f3d09701c27512f9d31..75ef74781e2f098982fff38b56e9e9e304e8d0f8 100644
--- a/src/colvar/Energy.cpp
+++ b/src/colvar/Energy.cpp
@@ -47,6 +47,7 @@ potential energy function. This is for instance not true when
 using GROMACS with lambda replica exchange of with plumed-hrex branch.
 
 \par Examples
+
 The following input instructs plumed to print the energy of the system
 \verbatim
 ENERGY LABEL=ene
diff --git a/src/colvar/Jcoupling.cpp b/src/colvar/Jcoupling.cpp
index 94e5b82a0b53b46927d29fb3c6d3e637cec7989b..7e23ce3b1a3dde102cec3c4fb1f80b2c87fd5b8b 100644
--- a/src/colvar/Jcoupling.cpp
+++ b/src/colvar/Jcoupling.cpp
@@ -58,6 +58,7 @@ and SHIFT keywords. You will need to make sure you are using the correct dihedra
 - CO-C\f$\gamma\f$: \f$\chi_1\f$
 
 \par Examples
+
 In the following example we calculate the Ha-N J-coupling from a set of atoms involved in
 dihedral \f$\psi\f$ angles in the peptide backbone. We also add the experimental datapoints and compute
 the correlation and other measures and finally print the results.
diff --git a/src/colvar/NOE.cpp b/src/colvar/NOE.cpp
index 69d9a3797ce2ffa5ae560bc3b42540f13efa7d83..1ad5291b7239589dced54cef3f70462035bca877 100644
--- a/src/colvar/NOE.cpp
+++ b/src/colvar/NOE.cpp
@@ -48,6 +48,7 @@ Intensities can then in principle ensemble averaged using \ref ENSEMBLE and used
 calculate a scoring function for example with \ref METAINFERENCE.
 
 \par Examples
+
 In the following examples three noes are defined, the first is calculated based on the distances
 of atom 1-2 and 3-2; the second is defined by the distance 5-7 and the third by the distances
 4-15,4-16,8-15,8-16.
diff --git a/src/colvar/PropertyMap.cpp b/src/colvar/PropertyMap.cpp
index 7ecb08b0cdf48104462f7da917a869523dd86173..1df4c0d3c3b3ac837c7e09bfa60f7d7b3e546a55 100644
--- a/src/colvar/PropertyMap.cpp
+++ b/src/colvar/PropertyMap.cpp
@@ -46,6 +46,7 @@ where the parameters \f$X_i\f$  and  \f$Y_i\f$ are provided in the input pdb (al
  \f$D_i(x)\f$  is the MSD after optimal alignment calculated on the pdb frames you input (see Kearsley).
 
 \par Examples
+
 \verbatim
 p3: PROPERTYMAP REFERENCE=../../trajectories/path_msd/allv.pdb PROPERTY=X,Y LAMBDA=69087 NEIGH_SIZE=8 NEIGH_STRIDE=4
 PRINT ARG=p3.X,p3.Y,p3.zzz STRIDE=1 FILE=colvar FMT=%8.4f
diff --git a/src/colvar/RDC.cpp b/src/colvar/RDC.cpp
index 067ea3f2cd2307c4ff270b0954f69b655dd063ab..55ede195e551db1ca00900f9220eb61cc0fc2dee 100644
--- a/src/colvar/RDC.cpp
+++ b/src/colvar/RDC.cpp
@@ -89,6 +89,7 @@ Replica-Averaged restrained simulations can be performed with this CV and the fu
 Additional material and examples can be also found in the tutorial \ref belfast-9
 
 \par Examples
+
 In the following example five N-H RDCs are defined and their correlation with
 respect to a set of experimental data is calculated and restrained. In addition,
 and only for analysis purposes, the same RDCs are calculated using a Single Value
diff --git a/src/colvar/Volume.cpp b/src/colvar/Volume.cpp
index 2a388d778bcc443bef7be08ee2681425f5c42187..966c3680bd9fb77bb3a07e7ff975992b1c133688 100644
--- a/src/colvar/Volume.cpp
+++ b/src/colvar/Volume.cpp
@@ -35,6 +35,7 @@ namespace colvar {
 Calculate the volume of the simulation box.
 
 \par Examples
+
 The following input tells plumed to print the volume of the system
 \verbatim
 VOLUME LABEL=vol
diff --git a/src/function/Combine.cpp b/src/function/Combine.cpp
index b74e1601421dee9da318cad663a1330f2d45a79b..d8f2e7fbb994841e7d0d4ce2d4e6132b0643b757 100644
--- a/src/function/Combine.cpp
+++ b/src/function/Combine.cpp
@@ -49,6 +49,7 @@ is periodic.
 
 
 \par Examples
+
 The following input tells plumed to print the distance between atoms 3 and 5
 its square (as computed from the x,y,z components) and the distance
 again as computed from the square root of the square.
diff --git a/src/function/Ensemble.cpp b/src/function/Ensemble.cpp
index b6b26b1c3b2f4130322426b40b6b5feb36f72136..f74e1aa67d4dab33387479b58bd3b93a34a96571 100644
--- a/src/function/Ensemble.cpp
+++ b/src/function/Ensemble.cpp
@@ -36,6 +36,7 @@ Calculates the replica averaging of a collective variable over multiple replicas
 Each collective variable is averaged separately and stored in a component labelled <em>label</em>.cvlabel.
 
 \par Examples
+
 The following input tells plumed to calculate the distance between atoms 3 and 5
 and the average it over the available replicas.
 \verbatim
diff --git a/src/function/LocalEnsemble.cpp b/src/function/LocalEnsemble.cpp
index e623be76a018b3bcf20a840ec2e180c121942c96..a17e9112e4b1019dbad29de834fd0adc5b2616d5 100644
--- a/src/function/LocalEnsemble.cpp
+++ b/src/function/LocalEnsemble.cpp
@@ -36,6 +36,7 @@ If more than one collective variable is given for each argument then they
 are averaged separately. The average is stored in a component labelled <em>label</em>.cvlabel.
 
 \par Examples
+
 The following input tells plumed to calculate the chemical shifts for four
 different proteins in the same simulation box then average them, calcualated
 the sum of the squared deviation with respect to the experiemntal values and
diff --git a/src/function/Piecewise.cpp b/src/function/Piecewise.cpp
index e3e147b69c69009d3ebfa54fac15cb739049483d..14b80e52c8e3f6f05134264e6b6ea75d9dea4d2c 100644
--- a/src/function/Piecewise.cpp
+++ b/src/function/Piecewise.cpp
@@ -55,6 +55,7 @@ in a vector of values. Each value will be named as the name of the original
 argument with suffix _pfunc.
 
 \par Examples
+
 \verbatim
 dist1: DISTANCE ATOMS=1,10
 dist2: DISTANCE ATOMS=2,11
diff --git a/src/function/Sort.cpp b/src/function/Sort.cpp
index 4636f3ad26ca0460150aca2bfac33d81def712f5..86c7c0fb0f3529cb81d28df98c2f019523cde568 100644
--- a/src/function/Sort.cpp
+++ b/src/function/Sort.cpp
@@ -41,6 +41,7 @@ This function sorts its arguments according to their magnitudes. The lowest argu
 labelled <em>label</em>.1, the second lowest will be labelled <em>label</em>.2 and so on.
 
 \par Examples
+
 The following input tells plumed to print the distance of the closest and of
 the farthest atoms to atom 1, chosen among atoms from 2 to 5
 \verbatim
diff --git a/src/function/Stats.cpp b/src/function/Stats.cpp
index 3513c9dcb852a5dcc4272de39ea7160b7f287f6d..45b9f0026b6b64e3177f5abc8489ed17b0c1aa8c 100644
--- a/src/function/Stats.cpp
+++ b/src/function/Stats.cpp
@@ -38,6 +38,7 @@ from other actions using PARARG (for example using experimental values from coll
 \ref CS2BACKBONE, \ref RDC, \ref NOE, \ref PRE).
 
 \par Examples
+
 The following input tells plumed to print the distance between three couple of atoms
 and compare them with three reference distances.
 
diff --git a/src/generic/DumpDerivatives.cpp b/src/generic/DumpDerivatives.cpp
index 7c1075cf11b5e032cd1f2da5d6c1b06f2147f1ac..5b49081a7c9d6fb8f09a9df289df24a5e7b6076a 100644
--- a/src/generic/DumpDerivatives.cpp
+++ b/src/generic/DumpDerivatives.cpp
@@ -40,6 +40,7 @@ will be output.  This command is most often used to test whether or not analytic
 can be done by outputting the derivatives calculated analytically and numerically.  You can control the buffering of output using the \ref FLUSH keyword.
 
 \par Examples
+
 The following input instructs plumed to write a file called deriv that contains both the
 analytical and numerical derivatives of the distance between atoms 1 and 2.
 \verbatim
diff --git a/src/generic/DumpForces.cpp b/src/generic/DumpForces.cpp
index 4a6aa3efb235dc2ccdf54afce997c704cf6bfe96..a5ae199e6fe9bac98fbbd28d2121e06ecb868c18 100644
--- a/src/generic/DumpForces.cpp
+++ b/src/generic/DumpForces.cpp
@@ -41,6 +41,7 @@ by specifying more than one argument. You can control the buffering of output us
 
 
 \par Examples
+
 The following input instructs plumed to write a file called forces that contains
 the force acting on the distance between atoms 1 and 2.
 \verbatim
diff --git a/src/generic/Flush.cpp b/src/generic/Flush.cpp
index e05159a03669e74d064a4e54370866faf77906a2..8b1be153ac417061de6b8232baf5c069cd83e3b1 100644
--- a/src/generic/Flush.cpp
+++ b/src/generic/Flush.cpp
@@ -40,6 +40,7 @@ storing data for printing in the buffers. Notice that wherever it is written in
 plumed input file, it will flush all the open files.
 
 \par Examples
+
 A command like this in the input will instruct plumed to flush all the output files every 100 steps
 \verbatim
 d1: DISTANCE ATOMS=1,10
diff --git a/src/generic/Print.cpp b/src/generic/Print.cpp
index 8542a978c9ccff0cdeca7ac0ee92b947e10e58f1..36a469023b3ea009d45bd8fd7db18f11673f0057 100644
--- a/src/generic/Print.cpp
+++ b/src/generic/Print.cpp
@@ -37,6 +37,7 @@ in the input so you can print files with different strides or print different qu
 to different files.  You can control the buffering of output using the \subpage FLUSH keyword.
 
 \par Examples
+
 The following input instructs plumed to print the distance between atoms 3 and 5 on a file
 called COLVAR every 10 steps, and the distance and total energy on a file called COLVAR_ALL
 every 1000 steps.
diff --git a/src/generic/UpdateIf.cpp b/src/generic/UpdateIf.cpp
index 086007f0cebfb34506da8c2ecbf51696dd5caf06..3f794dc373039f737032df35b955521a16a2979f 100644
--- a/src/generic/UpdateIf.cpp
+++ b/src/generic/UpdateIf.cpp
@@ -60,6 +60,7 @@ particular sense. For example, conditionally updating a \ref METAD keyword
 can lead to unexpected results.
 
 \par Examples
+
 The following input instructs plumed dump all the snapshots where an atom is in touch with
 the solute.
 \verbatim
diff --git a/src/gridtools/FourierTransform.cpp b/src/gridtools/FourierTransform.cpp
index d8509b27d270ade1d0f9542f5ec1dc68dbcf8639..38e4a1c0f6d8b315ebf6911656eb048f9d7cbf90 100644
--- a/src/gridtools/FourierTransform.cpp
+++ b/src/gridtools/FourierTransform.cpp
@@ -55,6 +55,7 @@ The keyword "FOURIER_PARAMETERS" deserves just a note on the usage. This keyword
 The default values of these parameters are: \f$a=1\f$ and \f$b=1\f$.
 
 \par Examples
+
 The following example tells Plumed to compute the complex 2D 'backward' Discrete Fourier Transform by taking the data saved on a grid called 'density', and normalizing the output by \f$ \frac{1}{\sqrt{N_x\, N_y}}\f$, where \f$N_x\f$ and \f$N_y\f$ are the number of data on the grid (it can be the case that \f$N_x \neq N_y\f$):
 
 \verbatim
diff --git a/src/multicolvar/DumpMultiColvar.cpp b/src/multicolvar/DumpMultiColvar.cpp
index 9a12d79d02b32abcfe14f47e2f8dd96a67462671..2a3b6a65c8687e5551847998cf5ad6f174daf238 100644
--- a/src/multicolvar/DumpMultiColvar.cpp
+++ b/src/multicolvar/DumpMultiColvar.cpp
@@ -45,6 +45,7 @@ namespace multicolvar {
 Dump atom positions and multicolvar on a file.
 
 \par Examples
+
 In this examples we calculate the distances between the  atoms of the first and the second
 group and we write them in the file MULTICOLVAR.xyz. For each couple it writes the
 coordinates of their geometric center and their distance.
diff --git a/src/setup/Units.cpp b/src/setup/Units.cpp
index 0be6e97379fd04d5ae6b44fb046c28196de0c9d8..890cecdae8582aa7c3fa8ecf4b279c96cb3a23b5 100644
--- a/src/setup/Units.cpp
+++ b/src/setup/Units.cpp
@@ -44,6 +44,7 @@ the units. For example, trajectories written in .gro format (with \ref DUMPATOMS
 are going to be always in nm.
 
 \par Examples
+
 \verbatim
 # this is using nm - kj/mol - fs
 UNITS LENGTH=nm TIME=fs
diff --git a/src/vatom/Ghost.cpp b/src/vatom/Ghost.cpp
index 3fa8c674e5a58de9e2237388143ee9fd67f039b9..0e9b73301bc34a8de95b0bca2cf4ffa77d27f706 100644
--- a/src/vatom/Ghost.cpp
+++ b/src/vatom/Ghost.cpp
@@ -37,6 +37,7 @@ The computed ghost atom is stored as a virtual atom that can be accessed in
 an atom list through the the label for the GHOST action that creates it.
 
 \par Examples
+
 The following input instructs plumed to print the distance between the
 ghost atom and the center of mass for atoms 15,20:
 \verbatim