Open ADFinput (see previous tutorials for this step). Select the 'N' nitrogen tool from the tool bar, and place nitrogen atom in the structure drawing area. Press Esc, and click in empty space so that nothing is selected. Similarly, choose 'H' hydrogen tool, and place hydrogen atom in the drawing area not too far away from the N atom (less than 10 Angstrom away). Add 2 more hydrogen atoms this way.
You should see one nitrogen and three hydrogen atoms in the drawing area now. For the purpose of the present tutorial, we intentionally do not add covalent bonding between the N and H atoms.
Starting from ADF version 2008, several new pre-optimization methods have been added. Below we will try to use two different methods to pre-optimize our ammonia molecule: the default simple force field, called MM in ADF GUI, and MOPAC. IMPORTANT: if you do not have MOPAC installed for ADF (contact your system administrator if you are not certain), create ammonia using the 'Structure Tool'. In this case, you can skip the rest of Step 1 and go straight to Step 2.
Select the SCM → Preferences command
This will invoke GUIprefs module, which will pop up in a separate window
In GUIprefs, select 'Pre-Optimizer' preset
The default option selected should be 'MM'.
If another option (not 'MM') for some reason was chosen, set this to 'MM' now Click 'Apply' or 'Save' at the bottom of the GUIprefs window.
'Apply' will apply the selected settings in all currently open GUI modules, without saving. Thus you can test your new settings witout overwriting your old preferences. 'Save' will record the new settings, and remember them even after you restart all the GUI units.
Go back to the ADFinput window and click 'Pre-Optimize' gear wheel button from the menu bar
Using the default pre-optimization algorithm (the only available method in ADF versions before 2008), the non-bonded atoms will 'fly away' from each other:
The default pre-optimization will finally stop with 'MM optimization ready' message. Apparently the result obtained is far away from the well-known anticipated NH3 molecule. To invoke one of the most effective pre-optimization methods introduced in ADF 2008, we will use GUIprefs module again:
Select 'MOPAC:' from 'Pre-optimize using' menu of GUIprefs window and check the 'Show' box of the 'Pre-optimizer output' option:
Click 'Apply' or 'Save' at the bottom of the GUIprefs window Get back to the ADFinput window Press 'Ctrl-Z'
The 'Ctrl-Z' will revert back to the original configuration of N and H atoms that you built, before the MM optimization.
Click 'Pre-Optimize' gear wheel button from the menu bar
The pre-optimizer will run, using MOPAC to optimize the geometry. This will produce a good-looking pyramidal ammonia molecule, with the N-H bond length of about 1.0 Angstrom. Additionally, it will create proper N-H covalent bonding! The message 'MOPAC optimization ready' will be displayed in the ADFinput window:
Because we checked the 'Show Pre-optimizer output' option, ADFtail will also pop up showing the MOPAC output. Those familiar with MOPAC can check the results in more detail.
