diff --git a/src/crystdistrib/QuaternionBondProductMatrix.cpp b/src/crystdistrib/QuaternionBondProductMatrix.cpp
index cf21f81f0b..dfada2bfe2 100644
--- a/src/crystdistrib/QuaternionBondProductMatrix.cpp
+++ b/src/crystdistrib/QuaternionBondProductMatrix.cpp
@@ -122,7 +122,7 @@ unsigned QuaternionBondProductMatrix::getNumberOfDerivatives() {
 }
 
 unsigned QuaternionBondProductMatrix::getNumberOfColumns() const {
-  const ActionWithMatrix* am=dynamic_cast<const ActionWithMatrix*>( getPntrToArgument(4)->getPntrToAction() ); plumed_assert( am ); 
+  const ActionWithMatrix* am=dynamic_cast<const ActionWithMatrix*>( getPntrToArgument(4)->getPntrToAction() ); plumed_assert( am );
   if( getPntrToArgument(4)->isSymmetric() && am->getNumberOfColumns()==getPntrToArgument(4)->getShape()[1]-1 ) return am->getNumberOfColumns() + 1;
   return am->getNumberOfColumns();
 }
@@ -245,15 +245,15 @@ void QuaternionBondProductMatrix::performTask( const std::string& controller, co
   }
   //had to split because bond's derivatives depend on the value of the overall quaternion component
   if( !doNotCalculateDerivatives() ) {
-      unsigned ostrn = getConstPntrToComponent(0)->getPositionInStream(); 
-      for(unsigned i=0; i<4; ++i) {
-        tempDot=dotProduct(Vector4d(quat[0],-quat[1],-quat[2],-quat[3]), dqt[1].getCol(i))*normFac;
-        if( i>0 ) {
-            plumed_assert( !stored[4+i] ); unsigned find = getPntrToArgument(4+i)->getIndexInStore( index1*getPntrToArgument(4+i)->getShape()[1] + ind2 );
-            myvals.addDerivative( ostrn, base + find, tempDot ); myvals.updateIndex( ostrn, base + find );
-        }
-        base += getPntrToArgument(4+i)->getNumberOfStoredValues();
+    unsigned ostrn = getConstPntrToComponent(0)->getPositionInStream();
+    for(unsigned i=0; i<4; ++i) {
+      tempDot=dotProduct(Vector4d(quat[0],-quat[1],-quat[2],-quat[3]), dqt[1].getCol(i))*normFac;
+      if( i>0 ) {
+        plumed_assert( !stored[4+i] ); unsigned find = getPntrToArgument(4+i)->getIndexInStore( index1*getPntrToArgument(4+i)->getShape()[1] + ind2 );
+        myvals.addDerivative( ostrn, base + find, tempDot ); myvals.updateIndex( ostrn, base + find );
       }
+      base += getPntrToArgument(4+i)->getNumberOfStoredValues();
+    }
   }
 
   //i component
@@ -269,19 +269,19 @@ void QuaternionBondProductMatrix::performTask( const std::string& controller, co
     if( doNotCalculateDerivatives() ) continue ;
     tempDot=(dotProduct(Vector4d(quat[1],quat[0],quat[3],-quat[2]), dqt[0].getCol(i)) + pref2*quatTemp[(5-i)%4])*normFac;
     addDerivativeOnVectorArgument( stored[i], 1, i,   index1, tempDot, myvals);
-    base += getPntrToArgument(i)->getNumberOfStoredValues(); 
+    base += getPntrToArgument(i)->getNumberOfStoredValues();
   }
 
-  if( !doNotCalculateDerivatives() ) { 
-      unsigned ostrn = getConstPntrToComponent(1)->getPositionInStream();
-      for(unsigned i=0; i<4; ++i) {
-        tempDot=dotProduct(Vector4d(quat[1],quat[0],quat[3],-quat[2]), dqt[1].getCol(i))*normFac;
-        if( i>0 ) { 
-            plumed_assert( !stored[4+i] ); unsigned find = getPntrToArgument(4+i)->getIndexInStore( index1*getPntrToArgument(4+i)->getShape()[1] + ind2 );
-            myvals.addDerivative( ostrn, base + find, tempDot+(-bond[i]*normFac*normFac*xf) ); myvals.updateIndex( ostrn, base + find );
-        }
-        base += getPntrToArgument(4+i)->getNumberOfStoredValues();
+  if( !doNotCalculateDerivatives() ) {
+    unsigned ostrn = getConstPntrToComponent(1)->getPositionInStream();
+    for(unsigned i=0; i<4; ++i) {
+      tempDot=dotProduct(Vector4d(quat[1],quat[0],quat[3],-quat[2]), dqt[1].getCol(i))*normFac;
+      if( i>0 ) {
+        plumed_assert( !stored[4+i] ); unsigned find = getPntrToArgument(4+i)->getIndexInStore( index1*getPntrToArgument(4+i)->getShape()[1] + ind2 );
+        myvals.addDerivative( ostrn, base + find, tempDot+(-bond[i]*normFac*normFac*xf) ); myvals.updateIndex( ostrn, base + find );
       }
+      base += getPntrToArgument(4+i)->getNumberOfStoredValues();
+    }
   }
 
 
@@ -303,15 +303,15 @@ void QuaternionBondProductMatrix::performTask( const std::string& controller, co
   }
 
   if( !doNotCalculateDerivatives() ) {
-      unsigned ostrn = getConstPntrToComponent(2)->getPositionInStream();
-      for(unsigned i=0; i<4; ++i) {
-        tempDot=dotProduct(Vector4d(quat[2],-quat[3],quat[0],quat[1]), dqt[1].getCol(i))*normFac;
-        if( i>0 ) {
-            plumed_assert( !stored[4+i] ); unsigned find = getPntrToArgument(4+i)->getIndexInStore( index1*getPntrToArgument(4+i)->getShape()[1] + ind2 );
-            myvals.addDerivative( ostrn, base + find, tempDot+(-bond[i]*normFac*normFac*yf) ); myvals.updateIndex( ostrn, base + find );
-        }
-        base += getPntrToArgument(4+i)->getNumberOfStoredValues();
+    unsigned ostrn = getConstPntrToComponent(2)->getPositionInStream();
+    for(unsigned i=0; i<4; ++i) {
+      tempDot=dotProduct(Vector4d(quat[2],-quat[3],quat[0],quat[1]), dqt[1].getCol(i))*normFac;
+      if( i>0 ) {
+        plumed_assert( !stored[4+i] ); unsigned find = getPntrToArgument(4+i)->getIndexInStore( index1*getPntrToArgument(4+i)->getShape()[1] + ind2 );
+        myvals.addDerivative( ostrn, base + find, tempDot+(-bond[i]*normFac*normFac*yf) ); myvals.updateIndex( ostrn, base + find );
       }
+      base += getPntrToArgument(4+i)->getNumberOfStoredValues();
+    }
   }
 
   //k component
@@ -337,8 +337,8 @@ void QuaternionBondProductMatrix::performTask( const std::string& controller, co
   for(unsigned i=0; i<4; ++i) {
     tempDot=dotProduct(Vector4d(quat[3],quat[2],-quat[1],quat[0]), dqt[1].getCol(i))*normFac;
     if( i>0 ) {
-        plumed_assert( !stored[4+i] ); unsigned find = getPntrToArgument(4+i)->getIndexInStore( index1*getPntrToArgument(4+i)->getShape()[1] + ind2 ); 
-        myvals.addDerivative( ostrn, base + find, tempDot+(-bond[i]*normFac*normFac*zf) ); myvals.updateIndex( ostrn, base + find );
+      plumed_assert( !stored[4+i] ); unsigned find = getPntrToArgument(4+i)->getIndexInStore( index1*getPntrToArgument(4+i)->getShape()[1] + ind2 );
+      myvals.addDerivative( ostrn, base + find, tempDot+(-bond[i]*normFac*normFac*zf) ); myvals.updateIndex( ostrn, base + find );
     }
     base += getPntrToArgument(4+i)->getNumberOfStoredValues();
   }
diff --git a/src/secondarystructure/AlphaRMSD.cpp b/src/secondarystructure/AlphaRMSD.cpp
index 9a5d6e7214..285b17d8e7 100644
--- a/src/secondarystructure/AlphaRMSD.cpp
+++ b/src/secondarystructure/AlphaRMSD.cpp
@@ -169,9 +169,9 @@ AlphaRMSD::AlphaRMSD(const ActionOptions&ao):
   readInputLine( lab + ": SECONDARY_STRUCTURE_RMSD BONDLENGTH=0.17" + seglist + structure + " " + atoms + " TYPE=" + type + nopbcstr );
   // Create the less than object
   if( ltmap.length()>0 ) {
-      readInputLine( getShortcutLabel() + "_lt: LESS_THAN ARG=" + lab + " SWITCH={" + ltmap  +"}");
-      if( uselessthan ) readInputLine( getShortcutLabel() + "_lessthan: SUM ARG=" + getShortcutLabel() + "_lt PERIODIC=NO");
-      else readInputLine( getShortcutLabel() + ": SUM ARG=" + getShortcutLabel() + "_lt PERIODIC=NO");
+    readInputLine( getShortcutLabel() + "_lt: LESS_THAN ARG=" + lab + " SWITCH={" + ltmap  +"}");
+    if( uselessthan ) readInputLine( getShortcutLabel() + "_lessthan: SUM ARG=" + getShortcutLabel() + "_lt PERIODIC=NO");
+    else readInputLine( getShortcutLabel() + ": SUM ARG=" + getShortcutLabel() + "_lt PERIODIC=NO");
   }
 }
 
diff --git a/src/secondarystructure/AntibetaRMSD.cpp b/src/secondarystructure/AntibetaRMSD.cpp
index d12fad3aa4..19cbada1ba 100644
--- a/src/secondarystructure/AntibetaRMSD.cpp
+++ b/src/secondarystructure/AntibetaRMSD.cpp
@@ -233,22 +233,22 @@ AntibetaRMSD::AntibetaRMSD(const ActionOptions&ao):
   std::string atoms="ATOMS=" + all_atoms[0]; for(unsigned i=1; i<all_atoms.size(); ++i) atoms += "," + all_atoms[i];
 
   if( strands_cutoff>0 ) {
-      readInputLine( scutoff_action ); std::string str_cut; Tools::convert( strands_cutoff, str_cut );
-      readInputLine( getShortcutLabel() + "_cut: CUSTOM ARG=" + getShortcutLabel() + "_cut_dists FUNC=step(" + str_cut + "-x) PERIODIC=NO");
-      readInputLine( lab + ": SECONDARY_STRUCTURE_RMSD ALIGN_STRANDS MASK=" + getShortcutLabel() + "_cut BONDLENGTH=0.17" + seglist + structure + " " + atoms + " TYPE=" + type + nopbcstr );
-      if( ltmap.length()>0 ) {
-          readInputLine( getShortcutLabel() + "_ltu: LESS_THAN ARG=" + lab + " SWITCH={" + ltmap  +"} MASK=" + getShortcutLabel() + "_cut");
-          readInputLine( getShortcutLabel() + "_lt: CUSTOM ARG=" + getShortcutLabel() + "_ltu," + getShortcutLabel() + "_cut FUNC=x*y PERIODIC=NO");
-      }
+    readInputLine( scutoff_action ); std::string str_cut; Tools::convert( strands_cutoff, str_cut );
+    readInputLine( getShortcutLabel() + "_cut: CUSTOM ARG=" + getShortcutLabel() + "_cut_dists FUNC=step(" + str_cut + "-x) PERIODIC=NO");
+    readInputLine( lab + ": SECONDARY_STRUCTURE_RMSD ALIGN_STRANDS MASK=" + getShortcutLabel() + "_cut BONDLENGTH=0.17" + seglist + structure + " " + atoms + " TYPE=" + type + nopbcstr );
+    if( ltmap.length()>0 ) {
+      readInputLine( getShortcutLabel() + "_ltu: LESS_THAN ARG=" + lab + " SWITCH={" + ltmap  +"} MASK=" + getShortcutLabel() + "_cut");
+      readInputLine( getShortcutLabel() + "_lt: CUSTOM ARG=" + getShortcutLabel() + "_ltu," + getShortcutLabel() + "_cut FUNC=x*y PERIODIC=NO");
+    }
   } else {
-      readInputLine( lab + ": SECONDARY_STRUCTURE_RMSD ALIGN_STRANDS BONDLENGTH=0.17" + seglist + structure + " " + atoms + " TYPE=" + type + nopbcstr );
-      if( ltmap.length()>0 ) readInputLine( getShortcutLabel() + "_lt: LESS_THAN ARG=" + lab + " SWITCH={" + ltmap  +"}");
+    readInputLine( lab + ": SECONDARY_STRUCTURE_RMSD ALIGN_STRANDS BONDLENGTH=0.17" + seglist + structure + " " + atoms + " TYPE=" + type + nopbcstr );
+    if( ltmap.length()>0 ) readInputLine( getShortcutLabel() + "_lt: LESS_THAN ARG=" + lab + " SWITCH={" + ltmap  +"}");
   }
   // Create the less than object
   if( ltmap.length()>0 ) {
-      if( uselessthan ) readInputLine( getShortcutLabel() + "_lessthan: SUM ARG=" + getShortcutLabel() + "_lt PERIODIC=NO");
-      else readInputLine( getShortcutLabel() + ": SUM ARG=" + getShortcutLabel() + "_lt PERIODIC=NO");
-  } 
+    if( uselessthan ) readInputLine( getShortcutLabel() + "_lessthan: SUM ARG=" + getShortcutLabel() + "_lt PERIODIC=NO");
+    else readInputLine( getShortcutLabel() + ": SUM ARG=" + getShortcutLabel() + "_lt PERIODIC=NO");
+  }
 }
 
 }
diff --git a/src/secondarystructure/ParabetaRMSD.cpp b/src/secondarystructure/ParabetaRMSD.cpp
index cf13cc9492..8e539a7b0e 100644
--- a/src/secondarystructure/ParabetaRMSD.cpp
+++ b/src/secondarystructure/ParabetaRMSD.cpp
@@ -275,25 +275,25 @@ ParabetaRMSD::ParabetaRMSD(const ActionOptions&ao):
   std::string atoms="ATOMS=" + all_atoms[0]; for(unsigned i=1; i<all_atoms.size(); ++i) atoms += "," + all_atoms[i];
 
   if( strands_cutoff>0 ) {
-      readInputLine( scutoff_action ); std::string str_cut; Tools::convert( strands_cutoff, str_cut );
-      readInputLine( getShortcutLabel() + "_cut: CUSTOM ARG=" + getShortcutLabel() + "_cut_dists FUNC=step(" + str_cut + "-x) PERIODIC=NO");
-      readInputLine( getShortcutLabel() + "_both: SECONDARY_STRUCTURE_RMSD ALIGN_STRANDS MASK=" + getShortcutLabel() + "_cut BONDLENGTH=0.17" + seglist + structure + " " + atoms + " TYPE=" + type + nopbcstr );
-      if( ltmap.length()>0 ) {
-         // Create the lowest line
-         readInputLine( lab + ": LOWEST ARG=" + getShortcutLabel() + "_both.struct-1," + getShortcutLabel() + "_both.struct-2" );
-         // Create the less than object
-         readInputLine( getShortcutLabel() + "_ltu: LESS_THAN ARG=" + lab + " SWITCH={" + ltmap  +"} MASK=" + getShortcutLabel() + "_cut"); 
-         // Multiply by the strands cutoff
-         readInputLine( getShortcutLabel() + "_lt: CUSTOM ARG=" + getShortcutLabel() + "_ltu," + getShortcutLabel() + "_cut FUNC=x*y PERIODIC=NO"); 
-      }
+    readInputLine( scutoff_action ); std::string str_cut; Tools::convert( strands_cutoff, str_cut );
+    readInputLine( getShortcutLabel() + "_cut: CUSTOM ARG=" + getShortcutLabel() + "_cut_dists FUNC=step(" + str_cut + "-x) PERIODIC=NO");
+    readInputLine( getShortcutLabel() + "_both: SECONDARY_STRUCTURE_RMSD ALIGN_STRANDS MASK=" + getShortcutLabel() + "_cut BONDLENGTH=0.17" + seglist + structure + " " + atoms + " TYPE=" + type + nopbcstr );
+    if( ltmap.length()>0 ) {
+      // Create the lowest line
+      readInputLine( lab + ": LOWEST ARG=" + getShortcutLabel() + "_both.struct-1," + getShortcutLabel() + "_both.struct-2" );
+      // Create the less than object
+      readInputLine( getShortcutLabel() + "_ltu: LESS_THAN ARG=" + lab + " SWITCH={" + ltmap  +"} MASK=" + getShortcutLabel() + "_cut");
+      // Multiply by the strands cutoff
+      readInputLine( getShortcutLabel() + "_lt: CUSTOM ARG=" + getShortcutLabel() + "_ltu," + getShortcutLabel() + "_cut FUNC=x*y PERIODIC=NO");
+    }
   } else {
-     readInputLine( getShortcutLabel() + "_both: SECONDARY_STRUCTURE_RMSD ALIGN_STRANDS BONDLENGTH=0.17" + seglist + structure + " " + atoms + " TYPE=" + type + nopbcstr );
-     if( ltmap.length()>0 ) {
-         // Create the lowest line
-         readInputLine( lab + ": LOWEST ARG=" + getShortcutLabel() + "_both.struct-1," + getShortcutLabel() + "_both.struct-2" );
-         // Create the less than object
-         readInputLine( getShortcutLabel() + "_lt: LESS_THAN ARG=" + lab + " SWITCH={" + ltmap  +"}");
-     } 
+    readInputLine( getShortcutLabel() + "_both: SECONDARY_STRUCTURE_RMSD ALIGN_STRANDS BONDLENGTH=0.17" + seglist + structure + " " + atoms + " TYPE=" + type + nopbcstr );
+    if( ltmap.length()>0 ) {
+      // Create the lowest line
+      readInputLine( lab + ": LOWEST ARG=" + getShortcutLabel() + "_both.struct-1," + getShortcutLabel() + "_both.struct-2" );
+      // Create the less than object
+      readInputLine( getShortcutLabel() + "_lt: LESS_THAN ARG=" + lab + " SWITCH={" + ltmap  +"}");
+    }
   }
   if( ltmap.length()>0 ) {
     if( uselessthan ) readInputLine( getShortcutLabel() + "_lessthan: SUM ARG=" + getShortcutLabel() + "_lt PERIODIC=NO");
diff --git a/src/secondarystructure/SecondaryStructureRMSD.cpp b/src/secondarystructure/SecondaryStructureRMSD.cpp
index 69c1b92506..f92e7b594c 100644
--- a/src/secondarystructure/SecondaryStructureRMSD.cpp
+++ b/src/secondarystructure/SecondaryStructureRMSD.cpp
@@ -122,7 +122,7 @@ SecondaryStructureRMSD::SecondaryStructureRMSD(const ActionOptions&ao):
   log<<"  Bibliography "<<plumed.cite("Pietrucci and Laio, J. Chem. Theory Comput. 5, 2197 (2009)"); log<<"\n";
 
   parseFlag("VERBOSE",verbose_output); parseFlag("ALIGN_STRANDS",align_strands);
-  log.printf("  ensuring atoms 7 and 22 in each residue are not separated by pbc before doing alignment\n"); 
+  log.printf("  ensuring atoms 7 and 22 in each residue are not separated by pbc before doing alignment\n");
 
   // Read in the atoms
   std::vector<AtomNumber> all_atoms; parseAtomList("ATOMS",all_atoms); requestAtoms( all_atoms );
diff --git a/src/valtools/VStack.cpp b/src/valtools/VStack.cpp
index e767fa85df..7d155cd263 100644
--- a/src/valtools/VStack.cpp
+++ b/src/valtools/VStack.cpp
@@ -49,7 +49,7 @@ class VStack : public ActionWithMatrix {
   unsigned getNumberOfColumns() const override { return getNumberOfArguments(); }
 ///
   void setupForTask( const unsigned& task_index, std::vector<unsigned>& indices, MultiValue& myvals ) const override ;
-/// 
+///
   int checkTaskIsActive( const unsigned& itask ) const override ;
 ///
   void performTask( const std::string& controller, const unsigned& index1, const unsigned& index2, MultiValue& myvals ) const override ;
@@ -135,7 +135,7 @@ void VStack::setupForTask( const unsigned& task_index, std::vector<unsigned>& in
 
 int VStack::checkTaskIsActive( const unsigned& itask ) const {
   return 1;
-} 
+}
 
 void VStack::performTask( const std::string& controller, const unsigned& index1, const unsigned& index2, MultiValue& myvals ) const {
   unsigned ind2 = index2; if( index2>=getConstPntrToComponent(0)->getShape()[0] ) ind2 = index2 - getConstPntrToComponent(0)->getShape()[0];