Re-ordering atoms in the internal matrix

In the previous example we had a nicely defined dihedral to work with, but this may of course not always be the case. The internal matrix builder of ADFinput adheres strictly to the order of the atoms present, and this may sometimes lead to undesirable internal matrices. Fortunately, we can re-order the atoms in order to achieve a more desirable internal matrix. As an example we will take propane.

Using the carbon tool, place three carbons in a row
Use the 'Add Hydrogen' command to add hydrogens on all the carbon atoms

Since the carbon atoms are ordered according to the way they are bonded, the internal matrix is nicely defined. However, what if you would want to define the distance between the two terminal carbon atoms?

Select the second carbon (C1) in the coordinates window 
Push the 'Move Atom(s) down' button

You can now directly use the distance between the two terminal carbon atoms in the internal matrix. Note that although the other carbon-carbon bond length is still defined, changing it will distort the structure more than previously.

Another way of achieving the same goal is by deleting the second carbon-carbon bond.

 
Revert to the previous atom-order by moving the third carbon atom up
Delete the bond between the second and third carbon atom

Again, the distance between the two terminal carbon atoms is defined. In general, the first atom of a nonbonded fragment will, in the internal matrix, be connected to the first atom in the list.