Multi-Level principles: Regions, QUILD, QMMM, Quality per region¶

Generate regions¶

Start ADFinput, and build an Acetone molecule (or search for it ...)

Select one of the methyl groups

Use the panel bar Model → Regions command

Click on the ‘+’ button to add a new region

Change the name ‘Region_1’ into ‘Methyl’ (the label is editable)

You have just defined a new region, with a name ‘Methyl’. In your molecule window you can see what atoms are part of this region: they are highlighted with semi-transparent spheres. Note that there are now (at least) two regions define: the region that you defined, and a region called ‘All’ that is always present. Obviously, the All region includes all atoms. If you created the acetone molecule via the search command, you may have a third region that was automatically made.

Now we will define yet another region: the rest of the molecule. One way to do this is just to select the atoms that should be part of it, and pressing the ‘+’ button as you did before. However, to demonstrate some of the things you can do with regions we will do it in another way:

Make sure you have only the All and the Methyl region; if you have more, press the ‘-‘ button in front of the region

Click the check button in the ‘All’ region

Click the ‘+’ button to create a new region, as you did before

Click the check button in the ‘Methyl’ region

Click the ‘-‘ button in the ‘Region_2’ line, on the right-hand side

Basically, what you just did: select all atoms, make a new region containing all atoms, select the atoms in the Methyl region, remove the selected atoms from the new region. By clicking on the select buttons in the regions you can easily verify that your regions are now as they should be.

Visualization options per region¶

You can easily change what regions, and atoms within that region look like:

Click in empty (drawing) space to clear the selection

Click in the check box in front of the ‘Methyl’ region name to uncheck it

You should observe that the ghost-like region visualization disappears. Please turn it back on:

Click in the check box in front of the ‘Methyl’ region name to check it

Click on the right arrow at the end of the ‘Region_2’ line

Use the ‘Sticks’ command from the menu that appears

Now anything in ‘Region_2’ will be visualized as sticks only. Obviously you could also select any of the other display options.

Using regions to group molecules for editing¶

You can use regions to group atoms together for editing. When changing the distance, angle or dihedral using the slider atoms that are in one region move together.

As an example, lets break the aceton molecule into three fragments by deleting the C-C bonds:

Delete the CC bonds

Note that one CH3 fragment and the CO group are still together in one region, and the other CH3 group is in its own region.

Select the C from the CO group and the C from the CH3 group that is in a different region

(use shift-click on an atom to add atoms to the selection)

Use the slider to change the distance between the selected carbons

Note that the CO group and the CH3 group in the same region move together, thus the regions act as a tool to group things together for editing (with the slider). This grouping also works when you want to change an angle using the slider.

To prepare for the next step of the tutorial, undo the changes you made in this step using the Undo function repeatedly:

Undo until the C-C bonds are present again

Generate ethanol in water¶

To demonstrate how to set up a QM/MM calculation using ADFinput, we will use ethanol in water as an example. This will also show you how to add explicit solvent molecules to your system:

Start ADFinput

Build an ethanol molecule

Pre-optimize the structure

Edit → Solvent Molecules...

Change the radius of the solvent sphere to a small value,

such that 10 solvent molecules will be generated

Click on ‘Add Solvent’

As you can see, ADFinput has generated 10 water molecules around your ethanol molecule. It also has created two regions: a Solute region containing the ethanol molecule, and a Solvent region containing the water molecules. The visualization option for the Solvent region is such that the water molecules will only be shown using a Wire-frame representation.

Set up the QM/MM calculation¶

The next step is to set up the QM/MM calculation:

ADF → QMMM: select the ‘QMMM’ panel

Select the ‘Solute’ region in the ‘QM Region’ pull-down menu

Change the QMMM Task to Geometry Optimization

Now you will have three tabs: the main QMMM tab that allows you to set QMMM details, the ‘ADF 1’ tab that is the setup for the ADF calculation for the Solute subsystem, and the ‘MM 5’ tab that sets up the MM calculation for the full system.

ADFinput is currently not very smart in setting the proper atom types for a MM calculation. So you will need to examine the atom types as they are generated in the MM input, and fix them if they are not correct. To fix this, if needed, use the Atom Inspector panel to set the Tripos (or Amber) atom types as needed.

Click on the ‘MM 5’ tab

Activate the ‘Run Script’ panel (in the panel bar Details)

Check the atom types (in the run script)

Run the QMMM calculation, and see results¶

Run your calculation File → Run

Show the optimization movie:

In the ADFinput window: SCM → Movie

Graph → Energy

Note that ADFmovie (and the other GUI modules) will only show the results for the QM part of your calculation.

To get detailed information on your QMMM calculation, you can check the output file using the SCM → Output command.

Introduction¶

To demonstrate how to set up a DIM/QM DRF calculation using ADFinput, we will use water in water as an example. DRF is a QM/MM method in which the MM atoms interact with the QM region via induced dipoles and static charges. DRF facilitates calculating the optical properties of molecules, in this case we will look at the solvent effect on excitation energies. Note that the geometry optimizations are not possible with DRF in ADF.

Gas phase excitation energies¶

Start ADFinput

Build a water molecule

Pre-optimize the structure

Use the ADF panel

Select the Single Point task

Use the panel bar Properties → Excitations (UV/Vis), CD command

For the ‘Type of excitations’ option, Select ‘SingletOnly’

Save as ‘Water’

File → Run

Solvent effects excitation energies using DRF¶

Edit → Solvent Molecules...

Change the radius of the solvent sphere to a value,

such that approximately 130 solvent molecules will be generated

Click on ‘Add Solvent’

Use the panel bar Model → DIM/QM command

For the ‘Method’ option, Select ‘DRF’

Click the check button ‘QM part’ for the Solute region

Click the check button ‘DIM part’ for the Solvent region

In the next step atomic charges for the DRF region are computed using MDC-Q charges (LDA functional, DZP basis set). The atomic polarizabilities are taken from a inner database including H, C, N, O, F, S, Cl, Br, I atoms.

For the ‘Select charges’ option, Select ‘MDC-Q’

Save as ‘Water_DRF’

File → Run

See the results¶

When the calculation is ready, select both the Water_DRF and the Water job in ADFjobs

Open ADFspectra: SCM → Spectra command

Axes → Horizontal Unit → eV

Note that having two jobs selected in ADFjobs opens both jobs in the same ADFspectra window. That is easy to compare results.

Alternatively (with the same result), open ADFspectra for one of the jobs, and use the Add command in the File menu.