1. Double-click the Materials Science icon
   • (No icon? See Starting Maestro)

Figure 2-1. Change Working Directory option.

2. Go to File > Change Working Directory
3. Find your directory, and click Choose
4. Pre-generated input and results files are included for running jobs or examining output. Download the zip file here: schrodinger.com/sites/default/files/s3/release/current/Tutorials/zip/qm_multistage.zip
5. After downloading the zip file, unzip the contents in your Working Directorythe location where files are saved for ease of access throughout the tutorial

Figure 2-2. Save Project panel.

6. Go to File > Save Project As
7. Change the File name to QM_multistage_tutorial, click Save
   • The project is now named QM_multistage_tutorial.prj

Figure 2-3. Importing starting structures.

In this tutorial we will be using a group of molecules that were formed using the Elemental Enumeration panel. If you would like to create these molecules yourself, you can do so by following the Elemental Enumeration tutorial.

8. Go to File > Import Structures
9. Navigate to where you downloaded the tutorial files and select starting_structures.mae and click Open
   • A new entry group containing 21 molecules is added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion

Figure 3-1. Including only one entry while selecting the entire entry group.

1. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries the entire entry group titled starting_structures (21)
   • Clicking the entry group will select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries all of the entries within it
   • tetracene_m:N_n:N appears in as the title in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed, (where m and n may vary case-by-base) and all of the entries in the group are selected(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries

Figure 3-2. Using structures from the project table for the QM Multistage workflow.

2. Go to Tasks > Materials > Quantum Mechanics > Molecular Quantum Mechanics > QM Multistage Workflow
   • The QM Multistage Workflow panel opens
3. For Use structures from, ensure that Project Table (21 selected entries) is chosen

Note: All of the stages and parameters defined in the subsequent steps will apply to all of the input structures, i.e. the panel enables not only multiple QM jobs per molecule but also multiple molecules.

Figure 3-3. Setting up the stages: Stage 1.

In this example, we will first run a pre-optimization at a relatively cheap level of theory, followed by a second optimization at a higher level of theory using the geometry and Hessian from the first optimization. We will include some standard property calculations in the second stage.

4. For the first Stage type, choose Optimization
5. The Name can be kept as the default stage_1
   • Changing the stage name can help keep track of steps in large workflows
6. Maintain the default B3LYP-D3 level of Theory
7. Change the Basis set to MIDIXL
   • This is a relatively small basis set with only 192 functions for the molecules in this set that is still known to produce good molecular geometries
   • You can read more about this basis set in the For Further Reading section
8. Go to the SCF tab

Note: In this specific example, the pre-optimization has little effect on the geometries. Nonetheless, this can be beneficial as a time-saving step in cases of molecules with greater conformational freedom.

Note: Hover the mouse over the basis set in the structures list to see the number of associated basis functions

For information and practice with functionals and basis sets in Jaguar, see the Introduction to Geometry Optimizations, Functionals and Basis Sets tutorial.

Figure 3-4. Setting up the stages: Stage 1 SCF.

9. In the SCF tab, change the maximum iterations to 100
   • Note that in this case, the default number of steps is more than sufficient
   • The number of iterations is changed to highlight this parameter, if an optimization fails, the first setting to try changing is the maximum number of allowed iterations
10. Go to the Solvation tab

Figure 3-5. Setting up the stages: Stage 1 Solvation.

It is practical to include implicit solvation in our calculations for the optimized geometry of the molecules as well as their properties.

11. From the drop-down menu, select PCM for the Solvent model
    • For more about the PCM model see the For Further Reading section
12. Ensure the Solvent is set to water
13. Uncheck Use robust convergence
    • If this is selected, if the optimization procedure fails a robust convergence protocol is triggered
    • The protocol can be expensive, so since this is a quick pre-optimization it will not be selected
14. Leave the remaining optimization defaults and click Append Stage
    • A second stage is added to the workflow
    • You may need to scroll up to find the starting point of the new stage:

Figure 3-6. Setting up the stages: Stage 2.

15. For the second Stage type, choose Optimization again
16. Keep Geometry from stage 1 and Hessian checked, but uncheck Wavefunction
    • The geometry and Hessian from the first stage will be used as the starting point for the second stage.
    • Wave function is unchecked because the two stages use different basis sets, making it difficult to reuse the previous wave function. This is not an issue with the Hessian.
    • Hessians are also more expensive to recalculate than the wave function.
17. For Theory, choose M06-2X
    • B3LYP-D3 and M06-2X are both good functionals for geometry optimizations, but the systems they perform best on vary, see the For Further Reading section for more details
18. For Basis set, choose CC-PVTZ
    • This is a triple-zeta basis set, the type of basis set that is considered a minimum to use for highly accurate quantum mechanical result
    • This basis set is much larger than the one used in the previous stage with 680 functionals, meaning this calculation will also take longer
19. Go to the SCF tab

Figure 3-7. Setting up the stages: Stage 2 SCF.

20. In the SCF tab, change the Accuracy level to Accurate
    • This setting has to do with the type of pseudospectral grid used in the calculation, see the documentation for more information
21. Change the Maximum iterations to 100
22. Go to the Solvation tab

Figure 3-8. Setting up the stages: Stage 2 Solvation.

23. From the drop-down menu, select PCM for the Solvent model
24. Ensure the Solvent is set to water

Figure 3-9. Adding additional keywords.

The most common settings are managed by the panel, but it is also possible to add Jaguar keywords manually. In this specific example, it is best practice to add the following keyword:

25. Scroll to the bottom of the stage, and in the Additional keywords section, input ncanorb=495
    • ncanorb is a Jaguar keyword that can be sure to enforce a consistent set of orbitals
    • We use it here because we are using a very large pseudopotential basis set so different number of orbitals can be assigned in different calculations - in order to have consistent relative energies and reuse information from our previous calculation we need a consistent set of orbitals
    • Note that the number itself, 495, in this case, was determined by first running the job without this command. For a more thorough explanation of the need for this keyword in this particular example, see the help documentation

Note: An option for a machine learning force field (MLFF) is available as an alternative via an Additional keyword. Additional information regarding MLFF can be found in the help documentation, on our website, or the QM Multistage Workflow panel documentation.

Figure 3-10. Setting up the stages: Properties. Running the job.

26. In the second stage, go to the Properties tab
27. Select Vibrational frequencies and Atomic electrostatic potential charges (ESP)
    • These properties will be calculated for each molecule
28. Check Use robust convergence
29. Change the Job name to qm_multi_isomers

This job takes over 14 hours on 21 CPUs. For convenience, pre-generated results are available. To continue the tutorial with the pre-generated results, do not run the job and proceed to Section 5.

If you prefer to run the job yourself, configure your job settings (). Note that depending on your CPU resources, this job can be run in a highly parallelized fashion. Once set up, click Run.

30. Close the QM Multistage Workflow panel

Figure 4-1. The entry list after importing.

If you ran the job yourself, skip Steps 1 and 2. Otherwise, follow these steps to import the pre-generated results:

1. From the main menu, go to File > Import Structures
2. Navigate to where you downloaded the tutorial files and Open qm_multi_isomers-out.maegz
   • A new group, QM_multi_isomers (42), containing the output from both stages for all 21 molecules is added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion

Figure 4-2. Filtering the stage_2 outputs.

Let’s suppose we are interested in:

• Confirming that the optimizations from Stage 2 are minima via analysis of the frequency calculations
• Comparing the energies of the isomers
• Visualizing the ESP charges

First, it will be useful to create a new group with just the stage 2 outputs.

3. In the Entry List, type stage_2 in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion search () function to filter the relevant entries.
   • The entries associated with the second stage are filtered
4. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries the 21 entries with Shift + Click
   • You can confirm you have selected(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries only the entries of interest by reading the Entries information at the bottom of the Entry List:

Figure 4-3. Duplicating entries.

5. Right-click on any of the selected(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries entries and click Duplicate > Into New Group
   • The Duplicate into New Group panel opens

Figure 4-4. Duplicating into a new group.

6. For New group title: input Stage 2_Outputs
7. For Location of new group: choose At top level > End of table
8. Click Duplicate
   • A new group is added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion titled Stage2_Outputs (21)
9. Close the search filter (using the button next to the search bar)
   • The new group is now found at the bottom of the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion

Figure 4-5. Adding the lowest frequency to the project table from the property tree.

We can now confirm that the optimizations have found energy minima by analyzing the lowest frequency from the vibrational analysis. More conveniently, we can analyze the lowest frequency for each molecule simultaneously in the project tabledisplays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data:

10. Open the Project Tabledisplays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data ()
11. Show the Property Tree ()
12. Expand Jaguar > Secondary and check Lowest Frequency (cm^-1)
    • Lowest Frequency is added as a column in the Project Tabledisplays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data
    • You can also directly search for the property using the search bar at the top of the Property Tree panel

A quick scan of the lowest frequencies for the 21 entries in the Stage2_Outputs group demonstrates that the molecules are indeed at their respective minima, indicated by positive values for all frequencies.

Figure 4-6. Calculating a new property.

We can proceed to compare the relative gas phase energies of the isomers. The default output is in Hartrees. Let’s convert to kcal/mol:

13. In the Project Tabledisplays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data, open the Property Calculator ()
    • The Project Tabledisplays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data Calculator opens
14. For Create, name the property Energy kcal/mol
15. Click Functions and choose hartrees_to_kcal/mol
    • The function appears
16. Click Properties and choose Gas Phase Energy
    • The property appears
17. Insert a closed parenthesis ()
18. Click Execute

Figure 4-7. Sorting the energies.

19. Click OK to the warning about missing data and Close the calculator
    • The gas phase energy is converted to kcal/mol and added to the Project Tabledisplays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data in a new column titled Energy kcal/mol
20. With the Stage2_Outputs (21) group selected(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries, right-click on the new Energy kcal/mol column and choose Sort Selected (Ascending)
    • The 21 energies are sorted from lowest to highest energy

Note: There is an option in the Tasks menu to run the Jaguar/QSite Energy Converter. After doing so, in the Property Tree under Jaguar > Secondary, there is an option to add Gas Phase Relative Energy (kcal/mol) to the Project Tabledisplays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data, which will give the energies of the conformers relative to the lowest energy species.

Figure 4-8. Scatter plot of the relative energies. 

We can plot the relative energies for further visualization.

21. In the Project Tabledisplays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data, open Manage Plots   ()
22. Click Create then select Scatterplot… from the menu that appears
    • The Create New Scatterplot window opens
23. For X-Axis, choose Entry ID
24. For Y-Axis, choose Energy kcal/mol
    • The scatter plot is populated with the data
25. Hover over a data point to see the 2D visualization of the molecule

Feel free to explore the options to stylize the scatter plot.

26. When you are ready, close the Scatter Plot viewer, Manage Plots and the Project Tabledisplays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data and return to the workspacethe 3D display area in the center of the main window, where molecular structures are displayed