diff --git a/src/analysis/Committor.cpp b/src/analysis/Committor.cpp
index f7bf8baab3235a642647abf3e4637c8efd9b4f4a..ab314c03ed1bd48b4637c4ec0b7a59903b1ede3d 100644
--- a/src/analysis/Committor.cpp
+++ b/src/analysis/Committor.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 602163ebae5a02875480cdd45b6f79e5c3f7ffc8..e52c5bf0ef8f2327ec39830fb870170f1d5a496a 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 2e62f77bf227e0cf6067cdf8879e7870bdef3485..f4db715eea96ce3bf622260e0d0f14e4f6f4a688 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.
 \plumedfile
diff --git a/src/bias/LWalls.cpp b/src/bias/LWalls.cpp
index 8785af9e31474f7a818edf9ed248c2542dd11a43..d42c9ee2079d14395e99b727afadc68137084478 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 bbb4be3319d5f95173c52266608e58b01db431f7..20a76b2dff5f249d57adb0c78272a6371c5a11a6 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 af00e1efcee2f107c75a5d4f6340efd7bf045883..c9b43936c4c39f53fac2b7b6004271d261f2aa05 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 76c35154bd6b648132fb5396ca88fec4f694edea..43acb41203336aa0807d467453d3f7ccdc4fd6a4 100644
--- a/src/bias/PBMetaD.cpp
+++ b/src/bias/PBMetaD.cpp
@@ -146,6 +146,7 @@ boundaries. Note that:
 Multiple walkers  \cite multiplewalkers can also be used. 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 4ab187ec8de51b6843a4d8f8c16a6f1ab3be1e23..4f49e10b04a3e02ffd06a5674129f1fbd35aada9 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 866002efa9cc27a8337c8e8d92ddb48f5f5688e4..11023898b190af00c0e0077e8dd0e2c397e032c3 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 15a2a1d674433977db791c7f45c53f6b6930bb6e..1d0dd07f5dadb9394f4c8b173a18134bffcc9b25 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
 \plumedfile
 cell: CELL
diff --git a/src/colvar/DHEnergy.cpp b/src/colvar/DHEnergy.cpp
index 5b66a59480f0adee0a52cf278af209ed4ae30417..011fb1f4e741e60a5f6480e9e8e705fd389a9a2c 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
+
 \plumedfile
 # 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 33d03d1643a56f94bc626dac5b676c632696e2d2..680ce6219b16c9134bfa5970a72e213534567df3 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
 \plumedfile
diff --git a/src/colvar/Energy.cpp b/src/colvar/Energy.cpp
index f502d4c02e4dfa74b414473725dae6273cc92f54..3d0321aa0d2b37efe23c79a7d63cbdbf7ac3d605 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
 \plumedfile
 ene: ENERGY
diff --git a/src/colvar/Jcoupling.cpp b/src/colvar/Jcoupling.cpp
index 4334ecfd2db22a3001cfcc531c0923d5c8cfeb8d..5f7807adafc672476d1b78557c2ce362d4a85b8b 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 8a777c3d0dce276e0b9724d0addeb3d81ed0c630..86e0585976d972ff082fb31bfa1f99b3a00df516 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 5a40811ccde5a59426deec018c69b61d5e44281c..f1bc27b3d3203dc7399dd45e1a39e5d24940591f 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
+
 \plumedfile
 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 48ef11022ddb2aee97670368a67f4cdd6bfdda2f..02a62ec1f186f8da05603fdb17f4bbd42ae62635 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 9a05ce2236d54af22a569b9ec644d23757fb60e5..4970e159eb2fde4c487b22b2b772e95db0aef675 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
 \plumedfile
 vol: VOLUME
diff --git a/src/function/Combine.cpp b/src/function/Combine.cpp
index e7de7194b5c7a2b1de60a5cef08c8d5f174fad5d..afe85394c8d53d33a09a7af44f72ba2837e83bc1 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 198f2fad391de5e2a016a9d77ed8597ec9fd6245..a41710d2d06556960c2e1f7977eb1b29d5f3aacf 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.
 \plumedfile
diff --git a/src/function/LocalEnsemble.cpp b/src/function/LocalEnsemble.cpp
index 223294dff02817ac08dc2ec40d2b0e416cc3de58..a0c03f87a9e267a565e2b5ddc0eeacd6a9aa9cac 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 9e216c6c39b600e57509d0821986a1172532ca1e..3c3c879177eae1cb5c872c8ea822a70525cbd73e 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
+
 \plumedfile
 dist1: DISTANCE ATOMS=1,10
 dist2: DISTANCE ATOMS=2,11
diff --git a/src/function/Sort.cpp b/src/function/Sort.cpp
index 51a2cfa82016e6d371b585fa2aef17b328a1ff69..8ef00cfc862ad925a7745eec35b06357330346f8 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
 \plumedfile
diff --git a/src/function/Stats.cpp b/src/function/Stats.cpp
index 5d057ddff0d1288575c1e364d26bd88be582301e..6188c463b3e574ecc050c1427f8d7b68286ac6c4 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 c6dbfe9789087833c07c09e8c69c6cb617b44283..167f2a19f714ef6c9364506cd0bed67ae2f9fe12 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.
 \plumedfile
diff --git a/src/generic/DumpForces.cpp b/src/generic/DumpForces.cpp
index 5be6068dfd29f5bf1a0d51ca49a0fe880fb956ee..818026b1f891577189776edf74824c15d451bf39 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.
 \plumedfile
diff --git a/src/generic/Flush.cpp b/src/generic/Flush.cpp
index 71e9a06d3e144e991373ce501fa3d450205caec4..1afb50065a9c71cec163c16b982bf90000afac4e 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
 \plumedfile
 d1: DISTANCE ATOMS=1,10
diff --git a/src/generic/UpdateIf.cpp b/src/generic/UpdateIf.cpp
index fa3fd2a7445dd1a6da071d3e84b18b5d0178b3a1..56481b50ddea1644e3bd4ce72fca8382e062014b 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.
 \plumedfile
diff --git a/src/gridtools/FourierTransform.cpp b/src/gridtools/FourierTransform.cpp
index 76108a7be1d392797c86b22ecd625c1b26b24be7..de836de7a111fa684f809932d7b8be223d9b8643 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$N_x \neq N_y\f$):
 
 \plumedfile
diff --git a/src/multicolvar/DumpMultiColvar.cpp b/src/multicolvar/DumpMultiColvar.cpp
index 4ee9f9c5093c85127977bd7df89022f12006f3d0..4d27a717d3978484caf9667ef67b1aa23ec11b2d 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 07d244e12ccfcf578b9b9c6c4c4c9de389860c79..3844fce8300e043efd8be3cd08d6cc7470cc91c2 100644
--- a/src/setup/Units.cpp
+++ b/src/setup/Units.cpp
@@ -45,7 +45,6 @@ are going to be always in nm.
 
 \par Examples
 
-
 \plumedfile
 # this is using nm - kj/mol - fs
 UNITS LENGTH=A TIME=fs
diff --git a/src/vatom/Ghost.cpp b/src/vatom/Ghost.cpp
index 435b54cb8e54b1516ef66b9486c66f650f2b8230..f6666dc8dfdf6e99f872e6218bf08a5f69f5bc77 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:
 \plumedfile