Toluene charges, movies, frequencies and normal modes

The MOPAC-GUI is basically the same set of programs as the ADF-GUI. We suggest you start with the more general GUI tutorials if you are not familiar with the ADF-GUI.

When saving a job and running, MOPAC will be executed. The MOPAC results (output and AUX file) will be converted to a .rkf result file, that allows visualization of the results with the GUI modules like ADFview, ADFmovie and ADFspectra. Results that may be visualized include geometry, optimization changes (with energy), charges, bond orders, frequencies and normal modes. Obviously the MOPAC output file is also available

This tutorial will give you an example how to use MOPAC via the MOPAC-GUI from SCM.

Set up Toluene in MOPACinput

Start ADFjobs
SCM → New Input
Switch to MOPAC mode (panel bar ADF → Mopac)
/scm-uploads/doc.2016/Tutorials/_images/t14_mopacsstart.png

We will now make a Toluene molecule. Most conveniently this is done by simply searching for it within the MOPAC-GUI:

Control/Command-F
Enter ‘toluene’ as search text
Select ‘Toluen’ (the second match) from the list of matches
Click once in the drawing area in empty space to clear the selection
/scm-uploads/doc.2016/Tutorials/_images/t14_toluene.png

Run interactively

In the Mopac Main panel you can see what options for MOPAC have been selected: by default a Geometry optimization will be performed, using the PM7 method. MOPAC will also calculate the bond orders, and the GUI will automatically update the molecular bonds using these calculated bond orders. To show this, we will first remove the bonds and then run MOPAC by pressing the Run button:

Bonds → Remove Bonds
Press the ‘Run’ button
/scm-uploads/doc.2016/Tutorials/_images/t14_tolueneinteractive.png

The geometry has been optimized, but as the starting geometry was very reasonable this did not lead to big changes. In the status area you can see that MOPAC used 17 iterations, and you can see the final heat of formation. And obviously the bonds reappeared. These bonds are actually based on the bond orders as calculated by MOPAC.

You can now also show the calculated atomic charges:

View → Atom Info → Mopac Charges → Show
/scm-uploads/doc.2016/Tutorials/_images/t14_tolueneinteractivecharges.png

To see the MOPAC output, check the ‘Show output’ check box. And there is another way to run MOPAC interactively: use the pre-optimizer button (the cog wheel).

Check the ‘Show output’ check box
Right-click on the cog-wheel (the pre-optimizer button), and select Mopac from the menu
/scm-uploads/doc.2016/Tutorials/_images/t14_mopacoutput.png

As the geometry already had been optimized, nothing much happens. Except the MOPAC output file will be opened and appear in a new window. This file actually starts with the AUX file, followed by the output file.

Close all windows except ADFjobs (no need to save your setup)

Save job and results: charges and movies

The previous section showed how to run MOPAC interactively, typically to be used as a pre-optimizer. However, you can also run the MOPAC calculation as a ‘real’ job. Then the result files will be saved, and you can analyze them with the GUI tools.

SCM → New Input
Panel bar ** ADF → Mopac**
Control/Command-F
Enter ‘toluene’ as search text
Select ‘Toluen’ (the second match) from the list of matches
Click once in the drawing area in empty space to clear the selection
Check the ‘Show output’ check box

Once again we have our Toluene molecule. Now to run it as a job simply use the Save and Run command from the menu:

File → Save, save the job with name ‘Toluene’
File → Run
When asked to read the new coordinates (when the calculation finishes), click Yes
SCM → Logfile

The logfile will show the progress of the calculation:

/scm-uploads/doc.2016/Tutorials/_images/t14_logfile.png
SCM → View
Properties → Atom Info → Atom Charge: Net (mopac) → Show
/scm-uploads/doc.2016/Tutorials/_images/t14_adfviewcharges.png

As the ‘Show Output’ check box has been checked, the Mopac output is available:

Close the ADFview window
SCM → Output
Scroll to the end
/scm-uploads/doc.2016/Tutorials/_images/t14_output.png

Now for a geometry optimization it might be interesting to see a movie of the progress of the optimization:

Close the ADFoutput window
SCM → Movie
Graph → Energy
/scm-uploads/doc.2016/Tutorials/_images/t14_movie.png

You can also use ADFmovie to get detailed information about the geometry (distances, angles and so on), just as for an ADF geometry optimization. If you don’t know how, check the more general GUI tutorials.

Close all windows except ADFjobs and the ADFinput window showing your MOPAC input

IR spectrum and normal modes

Now we will modify our MOPAC job to perform a frequencies calculation:

Activate the ADFinput window (MOPACinput)
In the Mopac Main panel, change the Task to ‘Frequencies’

File → Run
Answer ‘Yes’ to save your setup
Answer ‘Yes’ to acknowledge that you are saving over a previous job

The logfile will be shown, and will very soon show the job is ready,

SCM → Spectra

The calculated IR spectrum will be shown:

/scm-uploads/doc.2016/Tutorials/_images/t14_ir.png
Click on the peak with the highest intensity, which is found around 2766 cm-1.

The selected mode will be shown:

/scm-uploads/doc.2016/Tutorials/_images/t14_mode.png
Browse through the normal modes using the left and right arrow key

Try the alternative method:
Click on the normal mode of interest in the table

SCM → Quit All