Merge branch 'v2.3' into v2.4

src/colvar/Dipole.cpp

@@ -34,6 +34,11 @@ namespace colvar {
 /*
 Calculate the dipole moment for a group of atoms.
 
+\warning
+The atoms used for \ref DIPOLE calculation should be from a whole molecule.
+In case the molecule is broken by the host MD code, please use \ref WHOLEMOLECULES to reconstruct it before \ref DIPOLE calculation.
+
+
 \par Examples
 
 The following tells plumed to calculate the dipole of the group of atoms containing

src/colvar/PathMSD.cpp

@@ -37,6 +37,10 @@ This variable computes the progress along a given set of frames that is provided
 in input ("sss" component) and the distance from them ("zzz" component).
 (see below).
 
+\warning
+The molecule used for \ref PATHMSD calculation should be whole (both atoms used in alignment and in displacement calculation).
+In case it is broken by the host MD code, please use \ref WHOLEMOLECULES to reconstruct it before \ref PATHMSD calculation.
+
 \par Examples
 
 Here below is a case where you have defined three frames and you want to

src/colvar/PropertyMap.cpp

@@ -45,6 +45,10 @@ zzz=-\frac{1}{\lambda}\log(\sum_i  \exp(-\lambda D_i(x)))
 where the parameters \f$X_i\f$  and  \f$Y_i\f$ are provided in the input pdb (allv.pdb in this case) and
  \f$D_i(x)\f$  is the MSD after optimal alignment calculated on the pdb frames you input (see Kearsley).
 
+\warning
+The molecule used for \ref PROPERTYMAP calculation should be whole (both atoms used in alignment and in displacement calculation).
+In case it is broken by the host MD code, please use \ref WHOLEMOLECULES to reconstruct it before \ref PROPERTYMAP calculation.
+
 \par Examples
 
 \plumedfile

src/colvar/RMSD.cpp

@@ -128,6 +128,10 @@ all the atoms in the segment are assumed to be part of both the alignment and di
 Please note that there are a number of other methods for calculating the distance between the instantaneous configuration and a reference configuration
 that are available in plumed.  More information on these various methods can be found in the section of the manual on \ref dists.
 
+\warning
+The molecule used for \ref RMSD calculation should be whole (both atoms used in alignment and in displacement calculation).
+In case it is broken by the host MD code, please use \ref WHOLEMOLECULES to reconstruct it before \ref RMSD calculation.
+
 \par Examples
 
 The following tells plumed to calculate the RMSD distance between