diff --git a/src/colvar/Dimer.cpp b/src/colvar/Dimer.cpp
index 0659e07464b1c5a699241eaf9f72bedc0de12c0e..429cc5241c8d40d947d4351ee3cc18a041a216e5 100644
--- a/src/colvar/Dimer.cpp
+++ b/src/colvar/Dimer.cpp
@@ -40,7 +40,7 @@ namespace colvar {
 /*
 This CV computes the dimer interaction energy for a collection of dimers.
 
-Each dimer represents an atom, as described in the dimer paper \cite dimer-metad. 
+Each dimer represents an atom, as described in the dimer paper \cite dimer-metad.
 A system of N atoms is thus represented with N dimers, each
 Dimer being composed of two beads and eventually a virtual site representing its center of mass.
 
diff --git a/src/crystallization/Q3.cpp b/src/crystallization/Q3.cpp
index 1fbfa0a5f5397599d03d7aeaa10955efd006685f..c52139cc92a09486cff6bce6d6adadb65dc1a54f 100644
--- a/src/crystallization/Q3.cpp
+++ b/src/crystallization/Q3.cpp
@@ -88,7 +88,7 @@ PRINT ARG=q3.mean FILE=colvar
 
 //+PLUMEDOC MCOLVARF LOCAL_Q3
 /*
-Calculate the local degree of order around an atoms by taking the average dot product between the \f$q_3\f$ vector on the central atom and the \f$q_3\f$ vector 
+Calculate the local degree of order around an atoms by taking the average dot product between the \f$q_3\f$ vector on the central atom and the \f$q_3\f$ vector
 on the atoms in the first coordination sphere.
 
 The \ref Q3 command allows one to calculate one complex vectors for each of the atoms in your system that describe the degree of order in the coordination sphere
diff --git a/src/crystallization/Q4.cpp b/src/crystallization/Q4.cpp
index 989289465bc67d069f557ff15f326cb32b8dc517..91983f5b26dc6ee84edafcf9f5092aed45967063 100644
--- a/src/crystallization/Q4.cpp
+++ b/src/crystallization/Q4.cpp
@@ -88,7 +88,7 @@ PRINT ARG=q4.mean FILE=colvar
 
 //+PLUMEDOC MCOLVARF LOCAL_Q4
 /*
-Calculate the local degree of order around an atoms by taking the average dot product between the \f$q_4\f$ vector on the central atom and the \f$q_4\f$ vector 
+Calculate the local degree of order around an atoms by taking the average dot product between the \f$q_4\f$ vector on the central atom and the \f$q_4\f$ vector
 on the atoms in the first coordination sphere.
 
 The \ref Q4 command allows one to calculate one complex vectors for each of the atoms in your system that describe the degree of order in the coordination sphere
diff --git a/src/crystallization/Q6.cpp b/src/crystallization/Q6.cpp
index 7d17b85ed51bd80c4c721a1cfa1418f85d1c064b..e2bef72275a3e72a5ba0fbc5ce96be9c4596ee78 100644
--- a/src/crystallization/Q6.cpp
+++ b/src/crystallization/Q6.cpp
@@ -88,7 +88,7 @@ PRINT ARG=q6.mean FILE=colvar
 
 //+PLUMEDOC MCOLVARF LOCAL_Q6
 /*
-Calculate the local degree of order around an atoms by taking the average dot product between the \f$q_6\f$ vector on the central atom and the \f$q_6\f$ vector 
+Calculate the local degree of order around an atoms by taking the average dot product between the \f$q_6\f$ vector on the central atom and the \f$q_6\f$ vector
 on the atoms in the first coordination sphere.
 
 The \ref Q6 command allows one to calculate one complex vectors for each of the atoms in your system that describe the degree of order in the coordination sphere
diff --git a/src/crystallization/SimpleCubic.cpp b/src/crystallization/SimpleCubic.cpp
index e6d55fc8e1fc650bc775789e32e1365f14945876..e573472965c68fba270ec49c8203e499a642b3f0 100644
--- a/src/crystallization/SimpleCubic.cpp
+++ b/src/crystallization/SimpleCubic.cpp
@@ -32,7 +32,7 @@ namespace crystallization {
 
 //+PLUMEDOC MCOLVAR SIMPLECUBIC
 /*
-Calculate whether or not the coordination spheres of atoms are arranged as they would be in a simple 
+Calculate whether or not the coordination spheres of atoms are arranged as they would be in a simple
 cubic structure.
 
 We can measure how similar the environment around atom \f$i\f$ is to a simple cubic structure is by evaluating
diff --git a/src/drr/DynamicReferenceRestraining.cpp b/src/drr/DynamicReferenceRestraining.cpp
index d865a761a54c4a7e84c15c2003602230332dd96b..3ba641e3669b38e05907708eae20b77194694e44 100644
--- a/src/drr/DynamicReferenceRestraining.cpp
+++ b/src/drr/DynamicReferenceRestraining.cpp
@@ -45,8 +45,8 @@ namespace drr {
 
 //+PLUMEDOC EABFMOD_BIAS DRR
 /*
-Used to performed extended-system adaptive biasing force(eABF) \cite Lelievre2007 method 
-on one or more collective variables. This method is also 
+Used to performed extended-system adaptive biasing force(eABF) \cite Lelievre2007 method
+on one or more collective variables. This method is also
 called dynamic reference restraining(DRR) \cite Zheng2012 .
 
 For each collective variable \f$\xi_i\f$, a fictitious variable \f$\lambda_i\f$
diff --git a/src/function/Custom.cpp b/src/function/Custom.cpp
index 6d3107fb86c7863714f50e5c60c583588c6eeb0e..4e4e767737e782c25fdf9f5c0dcd2b374c217ad8 100644
--- a/src/function/Custom.cpp
+++ b/src/function/Custom.cpp
@@ -33,7 +33,7 @@ namespace function {
 /*
 Calculate a combination of variables using a custom expression.
 
-This action computes an  arbitrary function of one or more 
+This action computes an  arbitrary function of one or more
 collective variables. Arguments are chosen with the ARG keyword,
 and the function is provided with the FUNC string. Notice that this
 string should contain no space. Within FUNC, one can refer to the
diff --git a/src/function/FuncSumHills.cpp b/src/function/FuncSumHills.cpp
index d5a65a96f47ed0874676488335c802a65e14b344..f89a8c78be042dac65a97b1fe36855553b268755 100644
--- a/src/function/FuncSumHills.cpp
+++ b/src/function/FuncSumHills.cpp
@@ -40,9 +40,9 @@ namespace function {
 
 //+PLUMEDOC FUNCTION FUNCSUMHILLS
 /*
-This function is intended to be called by the command line tool sum_hills 
-and it is meant to integrate a HILLS file or an HILLS file interpreted as 
-a histogram i a variety of ways. Therefore it is not expected that you use this 
+This function is intended to be called by the command line tool sum_hills
+and it is meant to integrate a HILLS file or an HILLS file interpreted as
+a histogram i a variety of ways. Therefore it is not expected that you use this
 during your dynamics (it will crash!)
 
 In the future one could implement periodic integration during the metadynamics
diff --git a/src/function/Piecewise.cpp b/src/function/Piecewise.cpp
index 84f7727f6117682f8aac834500c92ae9e8212e32..415b4cba6ebcda710cbd3102b266fa0b4e70330d 100644
--- a/src/function/Piecewise.cpp
+++ b/src/function/Piecewise.cpp
@@ -31,7 +31,7 @@ namespace function {
 
 //+PLUMEDOC FUNCTION PIECEWISE
 /*
-Compute a piece wise straight line through its arguments that passes through 
+Compute a piece wise straight line through its arguments that passes through
 a set of ordered control points.
 
 For variables less than the first
diff --git a/src/function/Stats.cpp b/src/function/Stats.cpp
index 59ba5b11770343d8397f61b7eb954ad6bf123af3..49825ddfe761c08ef78ae1b4da546b93711a56f1 100644
--- a/src/function/Stats.cpp
+++ b/src/function/Stats.cpp
@@ -30,7 +30,7 @@ namespace function {
 //+PLUMEDOC FUNCTION STATS
 /*
 Calculates statistical properties of a set of collective variables with respect to a set of reference values.
-In particular it calculates and store as components the sum of the squared deviations, the correlation, the 
+In particular it calculates and store as components the sum of the squared deviations, the correlation, the
 slope and the intercept of a linear fit.
 
 The reference values can be either provided as values using PARAMETERS or using value without derivatives
diff --git a/src/generic/Group.cpp b/src/generic/Group.cpp
index 5b7c0e962e9c2c94e3dcb1d03d894b6367d1fe1e..aa78609272ae66884cb86418fe4cfd7375e61549 100644
--- a/src/generic/Group.cpp
+++ b/src/generic/Group.cpp
@@ -36,7 +36,7 @@ namespace generic {
 
 //+PLUMEDOC GENERIC GROUP
 /*
-Define a group of atoms so that a particular list of atoms can be referenced with a single label 
+Define a group of atoms so that a particular list of atoms can be referenced with a single label
 in definitions of CVs or virtual atoms.
 
 Atoms can be listed as comma separated numbers (i.e. `1,2,3,10,45,7,9`) , simple positive ranges
diff --git a/src/generic/WholeMolecules.cpp b/src/generic/WholeMolecules.cpp
index 0055f30842e81f078355d662e2c3bee306dea83f..3b931c83b7f32bf07fca1ac76df0de128e86b498 100644
--- a/src/generic/WholeMolecules.cpp
+++ b/src/generic/WholeMolecules.cpp
@@ -40,7 +40,7 @@ namespace generic {
 
 //+PLUMEDOC GENERIC WHOLEMOLECULES
 /*
-This action is used to rebuild molecules that can become split by the periodic 
+This action is used to rebuild molecules that can become split by the periodic
 boundary conditions.
 
 It is similar to the ALIGN_ATOMS keyword of plumed1, and is needed since some
diff --git a/src/multicolvar/FilterLessThan.cpp b/src/multicolvar/FilterLessThan.cpp
index 5f39cb6fc35f4254653bb9abce368ebca86c770c..30616a9c6594805a5f0f6eb0636315dfe0471d6d 100644
--- a/src/multicolvar/FilterLessThan.cpp
+++ b/src/multicolvar/FilterLessThan.cpp
@@ -77,7 +77,7 @@ for \ref MULTICOLVARDENS
 
 //+PLUMEDOC MFILTERS MFILTER_LESS
 /*
-This action can be used to filter the distribution of colvar values in a \ref mcolv 
+This action can be used to filter the distribution of colvar values in a \ref mcolv
 so that one can compute the mean and so on for only those multicolvars less than a tolerance.
 
 This action can be used to create a dynamic group of atom based on the value of a multicolvar.
diff --git a/src/multicolvar/FilterMoreThan.cpp b/src/multicolvar/FilterMoreThan.cpp
index 77ef47c37b67d51bdcfe654191fa83ad46aad39e..2e42485b2bbcef66d39ea73b194d6f9f6eeb323c 100644
--- a/src/multicolvar/FilterMoreThan.cpp
+++ b/src/multicolvar/FilterMoreThan.cpp
@@ -77,7 +77,7 @@ for \ref MULTICOLVARDENS
 
 //+PLUMEDOC MFILTERS MFILTER_MORE
 /*
-This action can be used to filter the distribution of colvar values in a \ref mcolv 
+This action can be used to filter the distribution of colvar values in a \ref mcolv
 so that one can compute the mean and so on for only those multicolvars more than a tolerance.
 
 This action can be used to create a dynamic group of atom based on the value of a multicolvar.
diff --git a/src/multicolvar/VolumeAround.cpp b/src/multicolvar/VolumeAround.cpp
index fc61a39a3381012d2de036f5536cbcf06e54c62d..4d9b54f8901ee7f169dd35742500387f927bafb1 100644
--- a/src/multicolvar/VolumeAround.cpp
+++ b/src/multicolvar/VolumeAround.cpp
@@ -25,7 +25,7 @@
 
 //+PLUMEDOC VOLUMES AROUND
 /*
-This quantity can be used to calculate functions of the distribution of collective 
+This quantity can be used to calculate functions of the distribution of collective
 variables for the atoms that lie in a particular, user-specified part of of the cell.
 
 Each of the base quantities calculated by a multicolvar can can be assigned to a particular point in three
diff --git a/src/multicolvar/VolumeBetweenContours.cpp b/src/multicolvar/VolumeBetweenContours.cpp
index ffa8b63f69b94c23ee938b4d01561395d584e736..a8c43e8da7aaf2ad56c10e06d7b4e0f80388dbe2 100644
--- a/src/multicolvar/VolumeBetweenContours.cpp
+++ b/src/multicolvar/VolumeBetweenContours.cpp
@@ -28,7 +28,7 @@
 
 //+PLUMEDOC VOLUMES INENVELOPE
 /*
-This quantity can be used to calculate functions of the distribution of collective 
+This quantity can be used to calculate functions of the distribution of collective
 variables for the atoms that lie in a region where the density of a certain type of atom is high.
 
 This collective variable can be used to determine whether colvars are within region where the density
diff --git a/src/multicolvar/VolumeCavity.cpp b/src/multicolvar/VolumeCavity.cpp
index 0d300cc1fb1e084aaa6c877a6d14a89f6898dba7..38a9479109cbda500a20cf0ff5e12fe4acae0cb5 100644
--- a/src/multicolvar/VolumeCavity.cpp
+++ b/src/multicolvar/VolumeCavity.cpp
@@ -28,7 +28,7 @@
 
 //+PLUMEDOC VOLUMES CAVITY
 /*
-This quantity can be used to calculate functions of the distribution of collective 
+This quantity can be used to calculate functions of the distribution of collective
 variables for the atoms that lie in a box defined by the positions of four atoms.
 
 Each of the base quantities calculated by a multicolvar can can be assigned to a particular point in three
diff --git a/src/multicolvar/VolumeInCylinder.cpp b/src/multicolvar/VolumeInCylinder.cpp
index 0b03cb0e337d6bd200a3543768cae7e6077d7af4..56e54e1ebd6fa832730009d4092544a91c7a69d3 100644
--- a/src/multicolvar/VolumeInCylinder.cpp
+++ b/src/multicolvar/VolumeInCylinder.cpp
@@ -26,7 +26,7 @@
 
 //+PLUMEDOC VOLUMES INCYLINDER
 /*
-This quantity can be used to calculate functions of the distribution of collective 
+This quantity can be used to calculate functions of the distribution of collective
 variables for the atoms that lie in a particular, user-specified part of of the cell.
 
 Each of the base quantities calculated by a multicolvar can can be assigned to a particular point in three
diff --git a/src/multicolvar/VolumeInSphere.cpp b/src/multicolvar/VolumeInSphere.cpp
index ee4b0ee27fd717792344cd8205816a0e0c45a93e..bcb224459c226e5b9e4ebd3c40acd4bbaeafe097 100644
--- a/src/multicolvar/VolumeInSphere.cpp
+++ b/src/multicolvar/VolumeInSphere.cpp
@@ -26,7 +26,7 @@
 
 //+PLUMEDOC VOLUMES INSPHERE
 /*
-This quantity can be used to calculate functions of the distribution of collective 
+This quantity can be used to calculate functions of the distribution of collective
 variables for the atoms that lie in a particular, user-specified part of of the cell.
 
 Each of the base quantities calculated by a multicolvar can can be assigned to a particular point in three
diff --git a/src/multicolvar/VolumeTetrapore.cpp b/src/multicolvar/VolumeTetrapore.cpp
index beb77c996cf2f6af0fc0774a364cdaf83b0d2eb3..c624f1f90aa6cee5385e7a9c1e7fd0946c927b59 100644
--- a/src/multicolvar/VolumeTetrapore.cpp
+++ b/src/multicolvar/VolumeTetrapore.cpp
@@ -28,7 +28,7 @@
 
 //+PLUMEDOC VOLUMES TETRAHEDRALPORE
 /*
-This quantity can be used to calculate functions of the distribution of collective variables 
+This quantity can be used to calculate functions of the distribution of collective variables
 for the atoms lie that lie in a box defined by the positions of four atoms at the corners of a tetrahedron.
 
 Each of the base quantities calculated by a multicolvar can can be assigned to a particular point in three
diff --git a/src/multicolvar/XDistances.cpp b/src/multicolvar/XDistances.cpp
index a8854a695297d83016159eb4b917550d4bca1923..4045db9dd4641eaaaded369b3e5a1f170cc51b68 100644
--- a/src/multicolvar/XDistances.cpp
+++ b/src/multicolvar/XDistances.cpp
@@ -34,7 +34,7 @@ namespace multicolvar {
 //+PLUMEDOC MCOLVAR XDISTANCES
 /*
 Calculate the x components of the vectors connecting one or many pairs of atoms.
-You can then calculate functions of the distribution of 
+You can then calculate functions of the distribution of
 values such as the minimum, the number less than a certain quantity and so on.
 
 \par Examples
@@ -81,7 +81,7 @@ PRINT ARG=d1.gt0.1
 //+PLUMEDOC MCOLVAR YDISTANCES
 /*
 Calculate the y components of the vectors connecting one or many pairs of atoms.
-You can then calculate functions of the distribution of 
+You can then calculate functions of the distribution of
 values such as the minimum, the number less than a certain quantity and so on.
 
 \par Examples
@@ -129,7 +129,7 @@ PRINT ARG=d1.gt0.1
 //+PLUMEDOC MCOLVAR ZDISTANCES
 /*
 Calculate the z components of the vectors connecting one or many pairs of atoms.
-You can then calculate functions of the distribution of 
+You can then calculate functions of the distribution of
 values such as the minimum, the number less than a certain quantity and so on.
 
 \par Examples
diff --git a/src/multicolvar/XYDistances.cpp b/src/multicolvar/XYDistances.cpp
index 51f1a40b9926fabb1071926504275ec5302d853a..8b66fee57919f25c406d0d7941a0a17e1e29aecc 100644
--- a/src/multicolvar/XYDistances.cpp
+++ b/src/multicolvar/XYDistances.cpp
@@ -34,7 +34,7 @@ namespace multicolvar {
 //+PLUMEDOC MCOLVAR XYDISTANCES
 /*
 Calculate distance between a pair of atoms neglecting the z-component.
-You can then calculate functions of the distribution of 
+You can then calculate functions of the distribution of
  values such as the minimum, the number less than a certain quantity and so on.
 
 \par Examples
@@ -55,7 +55,7 @@ PRINT ARG=d1.min
 //+PLUMEDOC MCOLVAR XZDISTANCES
 /*
 Calculate distance between a pair of atoms neglecting the y-component.
-You can then calculate functions of the distribution of  
+You can then calculate functions of the distribution of
 values such as the minimum, the number less than a certain quantity and so on.
 
 \par Examples
@@ -76,7 +76,7 @@ PRINT ARG=d1.min
 //+PLUMEDOC MCOLVAR YZDISTANCES
 /*
 Calculate distance between a pair of atoms neglecting the x-component.
-You can then calculate functions of the distribution of  
+You can then calculate functions of the distribution of
 values such as the minimum, the number less than a certain quantity and so on.
 
 \par Examples
diff --git a/src/setup/Units.cpp b/src/setup/Units.cpp
index a56376c66e763f049b4bb5603e54b4874b0e2c0b..7e3b694b307dcf4a98319285bfb7d9dee656756c 100644
--- a/src/setup/Units.cpp
+++ b/src/setup/Units.cpp
@@ -32,10 +32,10 @@ namespace setup {
 
 //+PLUMEDOC GENERIC UNITS
 /*
-This command sets the internal units for the code.  A new unit can be set by either 
-specifying a conversion factor from the plumed default unit or by using a string 
-corresponding to one of the defined units given below.  This directive MUST 
-appear at the BEGINNING of the plumed.dat file.  The same units must be used 
+This command sets the internal units for the code.  A new unit can be set by either
+specifying a conversion factor from the plumed default unit or by using a string
+corresponding to one of the defined units given below.  This directive MUST
+appear at the BEGINNING of the plumed.dat file.  The same units must be used
 throughout the plumed.dat file.
 
 Notice that all input/output will then be made using the specified units.
diff --git a/src/vatom/Ghost.cpp b/src/vatom/Ghost.cpp
index 8745a71c53236636a9e89a386dd731288ca279f8..776fa62cde203f47e9ff467b9d448e3d31bb88bf 100644
--- a/src/vatom/Ghost.cpp
+++ b/src/vatom/Ghost.cpp
@@ -31,7 +31,7 @@ namespace vatom {
 
 //+PLUMEDOC VATOM GHOST
 /*
-Calculate the absolute position of a ghost atom with fixed coordinates 
+Calculate the absolute position of a ghost atom with fixed coordinates
 in the local reference frame formed by three atoms.
 
 The computed ghost atom is stored as a virtual atom that can be accessed in
diff --git a/src/ves/TD_ProductDistribution.cpp b/src/ves/TD_ProductDistribution.cpp
index 594f21887d22cff29153ea513450e56a6e17a0f6..48785831ea070048c2909446510b44dc12782e3b 100644
--- a/src/ves/TD_ProductDistribution.cpp
+++ b/src/ves/TD_ProductDistribution.cpp
@@ -33,7 +33,7 @@ namespace ves {
 
 //+PLUMEDOC VES_TARGETDIST TD_PRODUCT_DISTRIBUTION
 /*
-Target distribution given by a separable product 
+Target distribution given by a separable product
 of one-dimensional distributions (static or dynamic).
 
 Employ a target distribution that is a separable product