diff --git a/src/colvar/Dipole.cpp b/src/colvar/Dipole.cpp
index 680ce6219b16c9134bfa5970a72e213534567df3..14b22574c7595b61f35c8cf01d425fa3f708d4d3 100644
--- a/src/colvar/Dipole.cpp
+++ b/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
diff --git a/src/colvar/PathMSD.cpp b/src/colvar/PathMSD.cpp
index 2a6ded47c468469368d30f029f446d5950c4a66e..e4e1acc7807f7e47302a66a92054cffe3d75d27e 100644
--- a/src/colvar/PathMSD.cpp
+++ b/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
diff --git a/src/colvar/PropertyMap.cpp b/src/colvar/PropertyMap.cpp
index e4a68e59130e8ca8d2eabbe37750932a882c3fec..5a0aacf300910280c5e15331df210f7e3ce280d7 100644
--- a/src/colvar/PropertyMap.cpp
+++ b/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
diff --git a/src/colvar/RMSD.cpp b/src/colvar/RMSD.cpp
index 50c6574bb4388c99dce090837457e2d010d80d82..c36441d9c8f22f32b61c8d691d2db2ae72fc3186 100644
--- a/src/colvar/RMSD.cpp
+++ b/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