More fixes for manual

src/colvar/DihedralCorrelation.cpp

@@ -54,9 +54,9 @@ If you want to calculate the dihedral correlations between multiple pairs of dih
 this action you would use an input like this one shown below:
 
 ```plumed
-d: DIHEDRAL_CORRELATION
+d: DIHEDRAL_CORRELATION ...
   ATOMS1=1,2,3,4,5,6,7,8
-  ATOMS2=5,6,7,8,9,10,11,12
+  ATOMS2=9,10,11,12,13,14,15,16
 ...
 PRINT ARG=d FILE=colvar 
 ```
@@ -132,6 +132,7 @@ DihedralCorrelation::DihedralCorrelation(const ActionOptions&ao):
   parseFlag("NOPBC",nopbc);
   pbc=!nopbc;
 
+  addValueWithDerivatives(); setNotPeriodic();
   if(pbc) log.printf("  using periodic boundary conditions\n");
   else    log.printf("  without periodic boundary conditions\n");
 }

src/colvar/Gyration.cpp

@@ -55,7 +55,7 @@ In the above input the weights in the expressions above are set equal to the ele
 approach is to use the masses of the atoms as in the input below:
 
 ```plumed
-g: GYRATION ATOMS=1-5 TYPE=RADIUS USEMASS
+g: GYRATION ATOMS=1-5 TYPE=RADIUS MASS_WEIGHTED
 # This input is equivalent
 # g: GYRATION ATOMS=1-5 TYPE=RADIUS WEIGHTS=@Masses
 PRINT ARG=g FILE=colvar

src/colvar/GyrationShortcut.cpp

@@ -87,9 +87,11 @@ void GyrationShortcut::registerKeywords( Keywords& keys ) {
   keys.addFlag("MASS",false,"calculate the center of mass");
   keys.addFlag("MASS_WEIGHTED",false,"set the masses of all the atoms equal to one");
   keys.addFlag("UNORMALIZED",false,"do not divide by the sum of the weights");
-  if( keys.getDisplayName()=="GYRATION" ) keys.setValueDescription("scalar","the radius that was computed from the weights");
-  else if( keys.getDisplayName()=="GYRATION_TENSOR" ) keys.setValueDescription("matrix","the gyration tensor that was computed from the weights");
-  keys.addActionNameSuffix("_FAST"); keys.needsAction("CENTER"); keys.needsAction("CONSTANT");
+  if( keys.getDisplayName()=="GYRATION" ) {
+      keys.setValueDescription("scalar","the radius that was computed from the weights");
+      keys.addActionNameSuffix("_FAST");
+  } else if( keys.getDisplayName()=="GYRATION_TENSOR" ) keys.setValueDescription("matrix","the gyration tensor that was computed from the weights");
+  keys.needsAction("CENTER"); keys.needsAction("CONSTANT");
   keys.needsAction("ONES"); keys.needsAction("MASS"); keys.needsAction("DISTANCE");
   keys.needsAction("COVARIANCE_MATRIX"); keys.needsAction("SELECT_COMPONENTS");
   keys.needsAction("SUM"); keys.needsAction("CUSTOM"); keys.needsAction("DIAGONALIZE");
@@ -102,7 +104,7 @@ GyrationShortcut::GyrationShortcut(const ActionOptions& ao):
 {
   bool usemass, phases; parseFlag("MASS",usemass); parseFlag("PHASES",phases);
   std::vector<std::string> str_weights; parseVector("WEIGHTS",str_weights); std::string wflab;
-  if( !phases ) {
+  if( !phases && getName()=="GYRATION" ) {
     if( usemass || str_weights.size()==0 || (str_weights.size()==1 && str_weights[0]=="@Masses") ) {
       std::string wt_str;
       if( str_weights.size()>0 ) {
@@ -121,8 +123,11 @@ GyrationShortcut::GyrationShortcut(const ActionOptions& ao):
   bool nopbc; parseFlag("NOPBC",nopbc); std::string pbcstr; if(nopbc) pbcstr = " NOPBC";
   std::string phasestr; if(phases) phasestr = " PHASES";
   // Create the geometric center of the molecule
-  std::string weights_str=" WEIGHTS=" + str_weights[0];
-  for(unsigned i=1; i<str_weights.size(); ++i) weights_str += "," + str_weights[i];
+  std::string weights_str=""; 
+  if( str_weights.size()>0 ) {
+      weights_str=" WEIGHTS=" + str_weights[0];
+      for(unsigned i=1; i<str_weights.size(); ++i) weights_str += "," + str_weights[i];
+  }
   readInputLine( getShortcutLabel() + "_cent: CENTER ATOMS=" + atlist + pbcstr + phasestr + weights_str );
   if( str_weights.size()==0 ) {
     wflab = getShortcutLabel() + "_w"; std::string str_natoms; Tools::convert( atoms.size(), str_natoms );

src/colvar/PCARMSD.cpp

@@ -50,8 +50,11 @@ Calculate the PCA components for a number of provided eigenvectors and an averag
 Information about this method can be found in the reference papers in the bibliography below.  An example input is provided below:
 
 ```plumed
-#SETTINGS INPUTFILES=regtest/basic/rt64-pca/average.pdb,regtest/basic/rt64-pca/eigenvec.pdb
-PCARMSD AVERAGE=regtest/basic/rt64-pca/average.pdb EIGENVECTORS=regtest/basic/rt64-pca/eigenvec.pdb
+#SETTINGS INPUTFILES=regtest/trajectories/pca/average.pdb,regtest/trajectories/pca/eigenvec.pdb
+PCARMSD ... 
+  AVERAGE=regtest/trajectories/pca/average.pdb 
+  EIGENVECTORS=regtest/trajectories/pca/eigenvec.pdb
+...
 ```
 
 This input performs optimal alignment at every step and reports the rmsd so you know if you are far or close from the average structure.

src/pamm/PAMM.cpp

@@ -62,8 +62,8 @@ In this example I will explain in detail what the following input is computing:
 MOLINFO MOLTYPE=protein STRUCTURE=regtest/pamm/rt-pamm-periodic/M1d.pdb
 psi: TORSION ATOMS1=@psi-2 ATOMS2=@psi-3 ATOMS3=@psi-4
 phi: TORSION ATOMS1=@phi-2 ATOMS2=@phi-3 ATOMS3=@phi-4
-p: PAMM ARG=phi,psi CLUSTERS=regtest/pamm/rt-pamm-periodic/2D-testc-0.75.pammp MEAN1={COMPONENT=1} MEAN2={COMPONENT=2}
-PRINT ARG=p.mean-1,p.mean-2 FILE=colvar
+p: PAMM ARG=phi,psi CLUSTERS=regtest/pamm/rt-pamm-periodic/2D-testc-0.75.pammp MEAN
+PRINT ARG=p-1_mean-1,p-2_mean FILE=colvar
 ```
 
 The best place to start our explanation is to look at the contents of the `2D-testc-0.75.pammp` file, which you can do