diff --git a/src/colvar/PathMSD.cpp b/src/colvar/PathMSD.cpp
index d9e941b7e874637b5288ae80fa25b28fefd5afac..e2e776678248a6aee17cb9ba1dd346b921b501ac 100644
--- a/src/colvar/PathMSD.cpp
+++ b/src/colvar/PathMSD.cpp
@@ -62,7 +62,7 @@ note that NEIGH_STRIDE=4 NEIGH_SIZE=8 control the neighbor list parameter (optio
 recommended for performance) and states that the neighbor list will be calculated every 4
 steps and consider only the closest 8 member to the actual md snapshots.
 
-This input must be accompanied by a REFERENCE PDB file in which the positions of each of the frames are specified 
+This input must be accompanied by a REFERENCE PDB file in which the positions of each of the frames are specified
 separated using either END or ENDMDL as shown below:
 
 \auxfile{file.pdb}
diff --git a/src/colvar/Position.cpp b/src/colvar/Position.cpp
index 120ec10197171e436be031d22623d44fdd6aea56..d95a9234f6ccad5fe1ea3c343ff5d169bddd784b 100644
--- a/src/colvar/Position.cpp
+++ b/src/colvar/Position.cpp
@@ -61,7 +61,7 @@ p: POSITION ATOM=3
 PRINT ARG=p.x,p.y,p.z
 \endplumedfile
 
-The reference position is specified in a pdb file like the one shown below 
+The reference position is specified in a pdb file like the one shown below
 
 \auxfile{ref.pdb}
 ATOM      3  HT3 ALA     2      -1.480  -1.560   1.212  1.00  1.00      DIA  H
diff --git a/src/dimred/ClassicalMultiDimensionalScaling.cpp b/src/dimred/ClassicalMultiDimensionalScaling.cpp
index eb982bbde33495f3be480bc89e22384d8744f78a..c9b07a2a636fc1ec43b64b75e858eaadc8ed37eb 100644
--- a/src/dimred/ClassicalMultiDimensionalScaling.cpp
+++ b/src/dimred/ClassicalMultiDimensionalScaling.cpp
@@ -52,7 +52,7 @@ The RMSD distance between atoms 1-256 have moved is used to measure the distance
 
 \plumedfile
 data: COLLECT_FRAMES ATOMS=1-256
-mat: EUCLIDEAN_DISSIMILARITIES USE_OUTPUT_DATA_FROM=data 
+mat: EUCLIDEAN_DISSIMILARITIES USE_OUTPUT_DATA_FROM=data
 mds: CLASSICAL_MDS USE_OUTPUT_DATA_FROM=mat NLOW_DIM=2
 OUTPUT_ANALYSIS_DATA_TO_COLVAR USE_OUTPUT_DATA_FROM=mds FILE=rmsd-embed
 \endplumedfile
diff --git a/src/dimred/PCA.cpp b/src/dimred/PCA.cpp
index 5988a635f6aec2daa87ce49f4bc7a3554495a90d..c343f0ef668f291fe19950e22915f9e5524ada51 100644
--- a/src/dimred/PCA.cpp
+++ b/src/dimred/PCA.cpp
@@ -64,7 +64,7 @@ will be performed at the end of the simulation.
 
 \plumedfile
 ff: COLLECT_FRAMES ATOMS=1-22 STRIDE=1
-pca: PCA USE_OUTPUT_DATA_FROM=ff METRIC=OPTIMAL NLOW_DIM=2 
+pca: PCA USE_OUTPUT_DATA_FROM=ff METRIC=OPTIMAL NLOW_DIM=2
 OUTPUT_PCA_PROJECTION USE_OUTPUT_DATA_FROM=pca FILE=PCA-comp.pdb
 \endplumedfile
 
@@ -86,8 +86,8 @@ d6: DISTANCE ATOMS=3,4
 rr: RESTRAINT ARG=d1 AT=0.1 KAPPA=10
 rbias: REWEIGHT_BIAS TEMP=300
 
-ff: COLLECT_FRAMES ARG=d1,d2,d3,d4,d5,d6 LOGWEIGHTS=rbias STRIDE=5 
-pca: PCA USE_OUTPUT_DATA_FROM=ff METRIC=EUCLIDEAN NLOW_DIM=2 
+ff: COLLECT_FRAMES ARG=d1,d2,d3,d4,d5,d6 LOGWEIGHTS=rbias STRIDE=5
+pca: PCA USE_OUTPUT_DATA_FROM=ff METRIC=EUCLIDEAN NLOW_DIM=2
 OUTPUT_PCA_PROJECTION USE_OUTPUT_DATA_FROM=pca STRIDE=100 FILE=PCA-comp.pdb
 \endplumedfile
 
diff --git a/src/function/FuncPathMSD.cpp b/src/function/FuncPathMSD.cpp
index e1ed3088ece87391b54fbd53bbf7d8f451cfcade..91a0e811fc805e62d2e5e16d75b48deda0ee7463 100644
--- a/src/function/FuncPathMSD.cpp
+++ b/src/function/FuncPathMSD.cpp
@@ -57,7 +57,7 @@ p1: FUNCPATHMSD ARG=t1,t2,t3 LAMBDA=500.0
 PRINT ARG=t1,t2,t3,p1.s,p1.z STRIDE=1 FILE=colvar FMT=%8.4f
 \endplumedfile
 
-For this input you would then define the position of the reference coordinates in three separate pdb files.  The contents of the 
+For this input you would then define the position of the reference coordinates in three separate pdb files.  The contents of the
 file frame_1.pdb are shown below:
 
 \auxfile{frame_1.pdb}
diff --git a/src/generic/FitToTemplate.cpp b/src/generic/FitToTemplate.cpp
index 9ece91d9895940d9a28f1e825a1fc4bacd4de32a..215918b66091bd687e3b6b3cf57ad1603e7422cc 100644
--- a/src/generic/FitToTemplate.cpp
+++ b/src/generic/FitToTemplate.cpp
@@ -133,8 +133,8 @@ END
 
 In the following example you see two completely equivalent way
 to restrain an atom close to a position that is defined in the reference
-frame of an aligned molecule. You could for instance use this command to calculate the 
-position of the center of mass of a ligand after having aligned the atoms to the reference 
+frame of an aligned molecule. You could for instance use this command to calculate the
+position of the center of mass of a ligand after having aligned the atoms to the reference
 frame of the protein that is determined by aligning the atoms in the protein to the coordinates
 provided in the file ref.pdb
 \plumedfile
diff --git a/src/generic/Group.cpp b/src/generic/Group.cpp
index 5df1ca6545e3fd788b9c791f4b60a842f75cbd1b..59b26c780d33341308f4bfde9bf0fdfaa7c32a00 100644
--- a/src/generic/Group.cpp
+++ b/src/generic/Group.cpp
@@ -79,7 +79,7 @@ PRINT ARG=c FILE=colvar
 
 Groups can be conveniently stored in a separate file.
 E.g. one could create a file named `groups.dat` which reads
-\plumedincludefile 
+\plumedincludefile
 # this is groups.dat
 o: GROUP ATOMS=1,4,7,11,14
 h: GROUP ATOMS=2,3,5,6,8,9,12,13
diff --git a/src/generic/Include.cpp b/src/generic/Include.cpp
index c5844a0fa8cb47c65d1c4975ce2de32b5308f131..84bec5cb2cce4e19af97114527d187bfbaa22e22 100644
--- a/src/generic/Include.cpp
+++ b/src/generic/Include.cpp
@@ -54,7 +54,7 @@ d: DISTANCE ATOMS=c1,c2
 PRINT ARG=d
 \endplumedfile
 where the content of file pippo.dat is
-\plumedincludefile 
+\plumedincludefile
 # this is pippo.dat
 c1: COM ATOMS=1-100
 c2: COM ATOMS=101-202
@@ -67,7 +67,7 @@ c: COORDINATION GROUPA=groupa GROUPB=groupb R_0=0.5
 METAD ARG=c HEIGHT=0.2 PACE=100 SIGMA=0.2 BIASFACTOR=5
 \endplumedfile
 Here `groups.dat` could be huge file containing group definitions such as
-\plumedincludefile 
+\plumedincludefile
 # this is groups.dat
 groupa: GROUP ...
   ATOMS={
@@ -98,7 +98,7 @@ Another case where INCLUDE is very useful is when running multi-replica simulati
 Here different replicas might have different input files, but perhaps a large part of the
 input is shared. This part can be put in a common included file. For instance you could have
 `common.dat`:
-\plumedincludefile 
+\plumedincludefile
 # this is common.dat
 t: TORSION ATOMS=1,2,3,4
 \endplumedincludefile
@@ -128,12 +128,12 @@ t: TORSION ATOMS=1,2,3,4
 INCLUDE FILE=other.inc
 \endplumedmultireplicafile
 Then `other.0.inc`:
-\plumedincludefile 
+\plumedincludefile
 # this is other.0.inc
 RESTRAINT ARG=t AT=1.0 KAPPA=10
 \endplumedincludefile
 And `other.1.inc`:
-\plumedincludefile 
+\plumedincludefile
 # this is other.1.inc
 RESTRAINT ARG=t AT=1.2 KAPPA=10
 \endplumedincludefile
diff --git a/src/gridtools/FindContour.cpp b/src/gridtools/FindContour.cpp
index ffde85fdf797127af670bf83903e432bb961f185..4831ca8920ec7cc98798980d42a9ce64544055c2 100644
--- a/src/gridtools/FindContour.cpp
+++ b/src/gridtools/FindContour.cpp
@@ -78,9 +78,9 @@ tfcc: MTRANSFORM_MORE DATA=fcc LOWMEM SWITCH={SMAP R_0=0.5 A=8 B=8}
 center: CENTER_OF_MULTICOLVAR DATA=tfcc
 
 dens: MULTICOLVARDENS ...
-  DATA=tfcc ORIGIN=center DIR=xyz 
+  DATA=tfcc ORIGIN=center DIR=xyz
   NBINS=80,80,80 BANDWIDTH=1.0,1.0,1.0 STRIDE=1 CLEAR=1
-... 
+...
 
 FIND_CONTOUR GRID=dens CONTOUR=0.5 FILE=mycontour.xyz
 \endplumedfile
diff --git a/src/gridtools/FindSphericalContour.cpp b/src/gridtools/FindSphericalContour.cpp
index ade04ae7f5d0b529d42751bc6ef4d18d844211e6..ea59b860a4ff39b41d108837895b0db7cd05041c 100644
--- a/src/gridtools/FindSphericalContour.cpp
+++ b/src/gridtools/FindSphericalContour.cpp
@@ -83,7 +83,7 @@ the droplet from the surrounding gas.  The value of the phase field on this isoc
 
 \plumedfile
 # Calculate coordination numbers
-c1: COORDINATIONNUMBER SPECIES=1-512 SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0} 
+c1: COORDINATIONNUMBER SPECIES=1-512 SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0}
 # Select coordination numbers that are more than 2.0
 cf: MFILTER_MORE DATA=c1 SWITCH={RATIONAL D_0=2.0 R_0=0.1} LOWMEM
 # Build a contact matrix
diff --git a/src/multicolvar/Bridge.cpp b/src/multicolvar/Bridge.cpp
index 2aca9dd880fe32b527366beb98c4f538d193c8d6..997ccc0219cc79ba765c7bf8205814a58ffec467 100644
--- a/src/multicolvar/Bridge.cpp
+++ b/src/multicolvar/Bridge.cpp
@@ -52,7 +52,7 @@ that are bridging between atoms 1-10 and atoms 11-20 and to print the value
 to a file
 
 \plumedfile
-w1: BRIDGE BRIDGING_ATOMS=100-200 GROUPA=1-10 GROUPB=11-20 SWITCH={RATIONAL R_0=0.2} 
+w1: BRIDGE BRIDGING_ATOMS=100-200 GROUPA=1-10 GROUPB=11-20 SWITCH={RATIONAL R_0=0.2}
 PRINT ARG=w1 FILE=colvar
 \endplumedfile
 
diff --git a/src/multicolvar/DihedralCorrelation.cpp b/src/multicolvar/DihedralCorrelation.cpp
index e5cc7288803c769773127339eb7849f9354c40e0..4460d24913073cdd9e97a0d4c426e2a82195caac 100644
--- a/src/multicolvar/DihedralCorrelation.cpp
+++ b/src/multicolvar/DihedralCorrelation.cpp
@@ -71,7 +71,7 @@ dih: DIHCOR ...
 ATOMS1=@phi-3,@psi-3
 ATOMS2=@psi-3,@phi-4
 ATOMS3=@phi-4,@psi-4
-... 
+...
 PRINT ARG=dih FILE=colvar STRIDE=10
 \endplumedfile
 
diff --git a/src/multicolvar/Distances.cpp b/src/multicolvar/Distances.cpp
index 5623609471e45801f0052a4d98beb5d52ac2de37..5fc6026921b0360ed77543ad802e60ee30596d15 100644
--- a/src/multicolvar/Distances.cpp
+++ b/src/multicolvar/Distances.cpp
@@ -43,7 +43,7 @@ Calculate the distances between one or many pairs of atoms.  You can then calcul
 The following input tells plumed to calculate the distances between atoms 3 and 5 and between atoms 1 and 2 and to
 print the minimum for these two distances.
 \plumedfile
-d1: DISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} 
+d1: DISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1}
 PRINT ARG=d1.min
 \endplumedfile
 (See also \ref PRINT).
@@ -109,7 +109,7 @@ d1: DISTANCES ...
  MORE_THAN={RATIONAL R_0=2.0}
  BETWEEN={GAUSSIAN LOWER=1.0 UPPER=2.0}
  MIN={BETA=500.}
-... 
+...
 PRINT ARG=d1.lessthan,d1.morethan,d1.between,d1.min FILE=colvar STRIDE=10
 \endplumedfile
 (see \ref DISTANCES and \ref PRINT)
diff --git a/src/multicolvar/InPlaneDistances.cpp b/src/multicolvar/InPlaneDistances.cpp
index d98b315a3b50065ca88a07c11bbcc2cac4c0f05a..1d264bb4950886886eba709453d593aa442fad9a 100644
--- a/src/multicolvar/InPlaneDistances.cpp
+++ b/src/multicolvar/InPlaneDistances.cpp
@@ -93,7 +93,7 @@ InPlaneDistances::InPlaneDistances(const ActionOptions&ao):
   setupMultiColvarBase( all_atoms );
 
   // Setup the multicolvar base
-  setupMultiColvarBase( all_atoms ); readVesselKeywords(); 
+  setupMultiColvarBase( all_atoms ); readVesselKeywords();
   // Check atoms are OK
   if( getFullNumberOfTasks()!=getNumberOfAtoms()-2 ) error("you should specify one atom for VECTORSTART and one atom for VECTOREND only");
   // And check everything has been read in correctly
diff --git a/src/multicolvar/XDistances.cpp b/src/multicolvar/XDistances.cpp
index 1fdb8ccd25eccd03f03269f9d6ff2845b21244d3..90d99c879b20b74a35c66eaacf61ffa04d6073a1 100644
--- a/src/multicolvar/XDistances.cpp
+++ b/src/multicolvar/XDistances.cpp
@@ -42,7 +42,7 @@ The following input tells plumed to calculate the x-component of the vector conn
 the x-component of the vector connecting atom 1 to atom 2.  The minimum of these two quantities is then
 printed
 \plumedfile
-d1: XDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} 
+d1: XDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1}
 PRINT ARG=d1.min
 \endplumedfile
 (See also \ref PRINT).
@@ -61,7 +61,7 @@ The following input tells plumed to calculate the x-components of all the distin
 between atoms 1, 2 and 3 (i.e. the vectors between atoms 1 and 2, atoms 1 and 3 and atoms 2 and 3).
 The average of these quantities is then calculated.
 \plumedfile
-d1: XDISTANCES GROUP=1-3 MEAN 
+d1: XDISTANCES GROUP=1-3 MEAN
 PRINT ARG=d1.mean
 \endplumedfile
 (See also \ref PRINT)
@@ -88,7 +88,7 @@ The following input tells plumed to calculate the y-component of the vector conn
 the y-component of the vector connecting atom 1 to atom 2.  The minimum of these two quantities is then
 printed
 \plumedfile
-d1: YDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} 
+d1: YDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1}
 PRINT ARG=d1.min
 \endplumedfile
 (See also \ref PRINT).
@@ -135,7 +135,7 @@ The following input tells plumed to calculate the z-component of the vector conn
 the z-component of the vector connecting atom 1 to atom 2.  The minimum of these two quantities is then
 printed
 \plumedfile
-d1: ZDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} 
+d1: ZDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1}
 PRINT ARG=d1.min
 \endplumedfile
 (See also \ref PRINT).
diff --git a/src/multicolvar/XYDistances.cpp b/src/multicolvar/XYDistances.cpp
index d05ca33e484de337c6a4db7790be43e8458359e5..e286aeccc7629f8e617c7b1738f78cfcdf48a87d 100644
--- a/src/multicolvar/XYDistances.cpp
+++ b/src/multicolvar/XYDistances.cpp
@@ -44,7 +44,7 @@ to atom 5 projected in the xy-plane and the projection of the length of the vect
 the vector connecting atom 1 to atom 2 in the xy-plane.  The minimum of these two quantities is then
 printed
 \plumedfile
-d1: XYDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} 
+d1: XYDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1}
 PRINT ARG=d1.min
 \endplumedfile
 (See also \ref PRINT).
@@ -66,7 +66,7 @@ to atom 5 projected in the xz-plane and the projection of the length of the vect
 the vector connecting atom 1 to atom 2 in the xz-plane.  The minimum of these two quantities is then
 printed
 \plumedfile
-d1: XZDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} 
+d1: XZDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1}
 PRINT ARG=d1.min
 \endplumedfile
 (See also \ref PRINT).
@@ -88,7 +88,7 @@ to atom 5 in the yz-plane and the projection of the length of the vector
 the vector connecting atom 1 to atom 2 in the yz-plane.  The minimum of these two quantities is then
 printed
 \plumedfile
-d1: YZDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} 
+d1: YZDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1}
 PRINT ARG=d1.min
 \endplumedfile
 (See also \ref PRINT).
diff --git a/src/multicolvar/XYTorsion.cpp b/src/multicolvar/XYTorsion.cpp
index 9f3bfdee338e1e9c2e6bb6586667ca994dabe9c6..8788ddeb00db7f8331ff1c26ee9d26996a1737fb 100644
--- a/src/multicolvar/XYTorsion.cpp
+++ b/src/multicolvar/XYTorsion.cpp
@@ -42,7 +42,7 @@ Calculate the torsional angle around the x axis from the positive y direction.
 The following input tells plumed to calculate the angle around the x direction between the positive y-axis and the vector connecting atom 3 to atom 5 and
 the angle around the x direction between the positive y axis and the vector connecting atom 1 to atom 2.  The minimum of these two quantities is then output
 \plumedfile
-d1: XYTORSIONS ATOMS1=3,5 ATOMS2=1,2 BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1} 
+d1: XYTORSIONS ATOMS1=3,5 ATOMS2=1,2 BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}
 PRINT ARG=d1.between
 \endplumedfile
 (See also \ref PRINT).
@@ -58,7 +58,7 @@ Calculate the torsional angle around the x axis from the positive z direction.
 The following input tells plumed to calculate the angle around the x direction between the positive z-axis and the vector connecting atom 3 to atom 5 and
 the angle around the x direction between the positive z direction and the vector connecting atom 1 to atom 2.  The minimum of these two quantities is then output
 \plumedfile
-d1: XZTORSIONS ATOMS1=3,5 ATOMS2=1,2 BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1} 
+d1: XZTORSIONS ATOMS1=3,5 ATOMS2=1,2 BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}
 PRINT ARG=d1.*
 \endplumedfile
 (See also \ref PRINT).
@@ -74,7 +74,7 @@ Calculate the torsional angle around the y axis from the positive x direction.
 The following input tells plumed to calculate the angle around the y direction between the positive x-direction and the vector connecting atom 3 to atom 5 and
 the angle around the y direction between the positive x axis and the vector connecting atom 1 to atom 2.  The minimum of these two quantities is then output
 \plumedfile
-d1: YXTORSIONS ATOMS1=3,5 ATOMS2=1,2 BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1} 
+d1: YXTORSIONS ATOMS1=3,5 ATOMS2=1,2 BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}
 PRINT ARG=d1.*
 \endplumedfile
 (See also \ref PRINT).
@@ -90,7 +90,7 @@ Calculate the torsional angle around the y axis from the positive z direction.
 The following input tells plumed to calculate the angle around the y direction between the positive z-direction and the vector connecting atom 3 to atom 5 and
 the angle around the y direction between the positive z direction and the vector connecting atom 1 to atom 2.  The minimum of these two quantities is then output
 \plumedfile
-d1: YZTORSIONS ATOMS1=3,5 ATOMS2=1,2 BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1} 
+d1: YZTORSIONS ATOMS1=3,5 ATOMS2=1,2 BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}
 PRINT ARG=d1.*
 \endplumedfile
 (See also \ref PRINT).
@@ -106,7 +106,7 @@ Calculate the torsional angle around the z axis from the positive x direction.
 The following input tells plumed to calculate the angle around the z direction between the positive x-direction and the vector connecting atom 3 to atom 5 and
 the angle around the z direction between the positive x-direction and the vector connecting atom 1 to atom 2.  The minimum of these two quantities is then output
 \plumedfile
-d1: ZXTORSIONS ATOMS1=3,5 ATOMS2=1,2 BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1} 
+d1: ZXTORSIONS ATOMS1=3,5 ATOMS2=1,2 BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}
 PRINT ARG=d1.*
 \endplumedfile
 (See also \ref PRINT).
diff --git a/src/ves/TD_Grid.cpp b/src/ves/TD_Grid.cpp
index 2c9f023fffc884961f7bf2dc0bf29aad7b00dcdf..17d7cd7682469399298865e8b5cd8b2e1105ca54 100644
--- a/src/ves/TD_Grid.cpp
+++ b/src/ves/TD_Grid.cpp
@@ -78,7 +78,7 @@ file.
 td: TD_GRID FILE=input-grid.data
 \endplumedfile
 
-The input grid is then specified using the usual format employed by PLUMED an example of which 
+The input grid is then specified using the usual format employed by PLUMED an example of which
 is shown below:
 
 \auxfile{input-grid.data}