Improved doc for COORDINATION and DHENERGY

src/colvar/Coordination.cpp

@@ -51,11 +51,12 @@ but it can be changed using the optional SWITCH option.
 To make your calculation faster you can use a neighbor list, which makes it that only a
 relevant subset of the pairwise distance are calculated at every step.
 
-If GROUPB is empty, it will sum the N*(N-1)/2 pairs in GROUPA. This avoids computing 
+If GROUPB is empty, it will sum the \f$\frac{N(N-1)}{2}\f$ pairs in GROUPA. This avoids computing 
 twice permuted indexes (e.g. pair (i,j) and (j,i)) thus running at twice the speed.
 
 Notice that if there are common atoms between GROUPA and GROUPB the switching function should be
-equal to one. These "self interactions" are discarded by plumed (since version 2.1).
+equal to one. These "self contacts" are discarded by plumed (since version 2.1),
+so that they actually count as "zero".
 
 
 \par Examples

src/colvar/CoordinationBase.cpp

@@ -38,7 +38,7 @@ void CoordinationBase::registerKeywords( Keywords& keys ){
   keys.add("optional","NL_CUTOFF","The cutoff for the neighbour list");
   keys.add("optional","NL_STRIDE","The frequency with which we are updating the atoms in the neighbour list");
   keys.add("atoms","GROUPA","First list of atoms");
-  keys.add("atoms","GROUPB","Second list of atoms");
+  keys.add("atoms","GROUPB","Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)");
 }
 
 CoordinationBase::CoordinationBase(const ActionOptions&ao):

src/colvar/DHEnergy.cpp

@@ -47,7 +47,13 @@ using a Debye-Huckel approximation defined as
 \f]
 
 This collective variable can be used to analyze or induce electrostatically driven reactions \cite do13jctc.
-The two atom groups should be disjointed. Notice that the value of the DHENERGY is returned in plumed units (see \ref UNITS).
+Notice that the value of the DHENERGY is returned in plumed units (see \ref UNITS).
+
+If GROUPB is empty, it will sum the N*(N-1)/2 pairs in GROUPA. This avoids computing 
+twice permuted indexes (e.g. pair (i,j) and (j,i)) thus running at twice the speed.
+
+Notice that if there are common atoms between GROUPA and GROUPB their interaction is discarded.
+
 
 \par Examples
 \verbatim