Added more examples to manual for TORSION

src/colvar/Torsion.cpp

@@ -63,6 +63,30 @@ PRINT ARG=t1,t2 FILE=colvar STRIDE=10
 
 Here, \@phi-3 tells plumed that you would like to calculate the \f$\phi\f$ angle in the third residue of the protein.
 Similarly \@psi-4 tells plumed that you want to calculate the \f$\psi\f$ angle of the 4th residue of the protein.
+
+Both of the previous examples specify that the torsion angle should be calculated based on the position of four atoms.  
+For the first example in particular the assumption when the torsion is specified in this way is that there are chemical
+bonds between atoms 1 and 2, atoms 2 and 3 and atoms 3 and 4. In general, however, a torsional angle measures the angle 
+between two planes, which have at least one vector in common.  As shown below, there is thus an alternate, more general, way 
+through which we can define a torsional angle:
+
+\plumedfile
+t1: TORSION VECTOR1=1,2 AXIS=3,4 VECTOR2=5,6
+PRINT ARG=t1 FILE=colvar STRIDE=20
+\endplumedfile
+
+This input instructs PLUMED to calculate the angle between the plane containing the vector connecting atoms 1 and 2 and the vector 
+connecting atoms 3 and 4 and the plane containing this second vector and the vector connecting atoms 5 and 6.  We can even use 
+PLUMED to calculate the torsional angle between two bond vectors around the z-axis as shown below:
+
+\plumedfile
+a0: FIXEDATOM AT=0,0,0
+az: FIXEDATOM AT=0,0,1
+t1: TORSION VECTOR1=1,2 AXIS=a0,az VECTOR2=5,6
+PRINT ARG=t1 FILE=colvar STRIDE=20
+\endplumedfile
+
+
 */
 //+ENDPLUMEDOC