1. To open the software, double-click on the Materials Science icon
   • (No icon? See Starting Maestro)
   • (No software? Get the latest version here)

 

Ensure that upon launching, the top of the interface reads “Maestro Materials Science - Scratch Project”

 

Note: The Maestro and Materials Science Maestro graphical user interfaces (GUIs) are different applications. This tutorial teaches an introduction to the Materials Science GUI, which is recommended for all materials science users.

Figure 1-2-1. Change Working Directory option.

For this tutorial, create a folder somewhere convenient to serve as your working directorythe location where files are saved.. For example, create a directory on your desktop named Intro_MS_Tutorial.

 

 

1. Go to File > Change Working Directory, navigate to the Intro_MS_Tutorial directory and click Choose
   • The Intro_MS_Tutorial directory is now your working directorythe location where files are saved.

Figure 1-2-2. Save Project panel.

A project (.prj) can be saved with whatever name you prefer. In this instance (and quite often), we will name the project the same as the name of the working directory.

2. Go to File > Save Project As
3. For File Name input Intro_MS_Tutorial
4. Click Save
   • The project is now named Intro_MS_Tutorial.prj
   • The .prj file is now located in your working directorythe location where files are saved.
5. 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/intro_maestro_materialsscience.zip
6. 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 1-2-3. Importing.

One of the files now in your working directory is startermolecules.mae, which we will proceed to import. The .mae file type is a native MS Maestro structure file containing one or more structure models.

7. Go to File > Import Structures
8. Navigate to the working directory (if not already there), and select startermolecules.mae
9. Click Open

 

Note: You can also import structures by dragging files directly into MS Maestro.

Note: In addition to the .mae file type (discussed in detail here), other commonly used file types in MS Maestro include .in, .sh, .log, .out and .cms (discussed in detail here) among many others.

Figure 1-2-4. After the import. Note: If importing from the Sample Files menu, the import will include additional entries for use later in the tutorial.

A new group appears in the entry list entitled startermolecules (4), which contains four entries. A dimethylpyridine molecule is shown in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed.. In the next section, we will define these various terms (entry list, entries, workspace, etc.).

Note: Alternatively, all of the files for this tutorial are also available directly in the software via Help > Sample Files > Introductory Tutorial

Figure 1-4-1. Rotation.

The left mouse button is for selecting (covered in Section 1.5) and for rotating structures in the workspace.

1. Left-Click on any empty space in the workspace and while holding the button down, drag the mouse to rotate the structure in place.

 

 

Note: Unless specified otherwise, whenever you are instructed to “click”, you can assume it is a left-click.

Figure 1-4-2. Translation.

The center mouse button (the clickable scroll wheel or trackball) is for translating structures in the workspace.

2. Center-Click anywhere in the workspace and while holding the button down, drag the mouse to translate the structure in space
3. To re-center the structure in your workspace, either click the Fit button () in the toolbar, or press z on your keyboard

Figure 1-4-3. Zooming.

The right mouse button is for right-clicking to access additional menus (to be used later) and for zooming in the workspace.

4. Right-click on any empty space in the workspace and while holding the button down, drag the mouse to zoom in or out on the structure
5. To re-fit the structure in your workspace, either click the Fit button () in the toolbar, or press z on your keyboard

Figure 1-5-1. Current entry list with dimethylpyridine included.

The entry list currently contains one entry group (startermolecules (4)) which contains four entries (dimethylpyridine, TiCl4, poly(styrene) and AlphaQuartz).

 

Because the blue circle is filled next to dimethylpyridine, we see its structure in the Workspace. We refer to this as the includedthe entry is represented in the Workspace, the circle in the In column is blue. structure. Whichever structure is includedthe entry is represented in the Workspace, the circle in the In column is blue. appears in the workspace.

Figure 1-5-2. Include TiCl4.

1. Click the empty circle next to the TiCl4 entry to includethe entry is represented in the Workspace, the circle in the In column is blue. this structure instead of the dimethylpyridine molecule
   • The circle next to TiCl4 is now filled blue, and the structure appears in the workspace

 

Note: You can include multiple entries simultaneously by holding Shift and clicking several circles in your entry list. The structures will overlap in the workspace. In the Workspace Configuration Tools, you can use the Tile option to show multiple structures.

Figure 1-5-3. Select TiCl4.

Upon import, all four entries were highlighted in the entry list. We refer to this row highlighting as selection.

2. Click the row containing TiCl4 in the entry list
   • It is highlighted in blue
   • Only TiCl4 is now 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.

 

MS Maestro uses a “select-first paradigm”, meaning that the TiCl4 entry is now ready to be operated on.

 

Note: You can select multiple entries simultaneously by holding Shift and clicking several rows in your entry list, or you can select an entire group at once by clicking on the entry group title.

 

Note: Selecting and including in the entry list are independent, meaning that an entry can be included and selected, but it can also be just included or just selected.

Figure 1-5-4. Select a chlorine atom.

In addition to being able to select entries in the entry list, we also use the term selection to refer to selecting components within the workspace, for example atoms or molecules.

3. In the Toolbar, ensure that Atoms is set as the selection scope (See Figure)
   • If not, click the dropdown and choose Atoms
4. In the Workspace, click on one of the chlorine atoms to select it
   • A box appears around the chlorine atom indicating that it is selected
   • If you hover over the chlorine atom, the Status Bar updates

 

Note: The selection scope dropdown includes atoms, repeating units, chains, molecules and entries - which are convenient ways to efficiently select species in the workspace.

Figure 1-5-5. Color a chlorine atom.

This chlorine atom is now selected, and can be modified. Again, MS Maestro uses a “select-first paradigm”, meaning that this chlorine atom is now ready to be operated on. For example, we can change the color of this chlorine atom to a lighter shade of green.

 

5. With the chlorine atom selected, in the Toolbar, click on the Style palette
6. Click on the Paint selected atoms one color button (paint bucket icon)
7. Choose a lighter shade of green
   • The color of the selected chlorine atom is changed

Figure 1-5-6. Select the remaining chlorine atoms.

You can use multiple selections to act on several atoms or molecules at once.

8. Select the remaining three chlorine atoms using Shift + Click

Figure 1-5-7. TiCl4 molecule with updated coloring.

9. Repeat the above steps to update the color of these atoms to match the first chlorine

 

 

Figure 1-5-8. Selection options in the Toolbar.

Note: Numerous modes for workspace selection are possible using the selection capabilities in the toolbar. For example, to accomplish selecting the four chlorine atoms in TiCl4, you could also use other approaches:

• Use the All button (all five atoms will be selected) and then deselect just the Ti atom with Command + Click (Ctrl + Click on Windows)
• Use the Quick Select dropdown to select the Metal Atoms (the Ti atom will be selected), and then the Invert button to select the chlorine atoms instead

Feel free to explore these capabilities to get familiar with selection.

Figure 1-5-9. Modifying the entry list.

The entry list can be modified and customized to keep your project structured.

• To change the name of an entry, double-click on its name in the entry row (if it is already selected, a single click will suffice)
• To change the order of entries, click, hold and drag to move a row
• Right-click on any entry to access several additional capabilities, including splitting, duplicating, deleting and grouping

 

Feel free to explore these capabilities to get familiar with organizing your entry list. We will not use these structures again in the tutorial, so do not worry about making any changes. You can also always import the starting .mae file again if you wish to revisit any of the above steps.

Figure 1-5-10. Updated entry list.

Optional Exercise: Try to duplicate TiCl4, rename it as TiCl4_new and then group these two structures in a new entry group called organometallics

 

Steps: Duplicate by right-clicking on the entry, rename by double-clicking on the name and group by selecting the entries to be grouped and right-clicking.

Figure 2-1-1. An optimized benzaldehyde structure in the workspace.

We will import a benzaldehyde molecule to explore some universal building tools.

1. In the main menu, go to File > Import Structures
   • The Import panel opens
2. Navigate to where you downloaded the tutorial files. Choose benzaldehyde.mae (inside the Section_02 directory)
3. Click Open
   • The benzaldehyde molecule is includedthe entry is represented in the Workspace, the circle in the In column is blue. in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed. and 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. in the entry list

Figure 2-1-2. Accessing the Measure tool from the Favorites bar.

4. In the Favorites toolbar, click Measure
   • A dropdown banner appears at the top of the workspace
   • By default, the Measure is set to Distances

Figure 2-1-3. Measuring the CO distance.

5. Pick the oxygen atom (in the aldehyde functional group) and its bound carbon atom 
   • The distance: 1.22 Å appears on the bond

Figure 2-1-4. Measuring an angle.

6. Change the measure option to Angles
7. Pick any three atoms to measure the corresponding angle
   • The angle measure appears
8. Click OK to close the measurement banner

 

Note: Labels can be toggled on and off using the ruler icon () at the bottom of the workspace. Hovering over the ruler icon, there is another icon (). Clicking on the … shows an extended menu that can be used to see any measured values.

Figure 2-1-5. Right-click on a measurement.

Keep the labels toggled on. If you right-click on any of the measures, you will see options to manually adjust and more. This can be a useful methodology for preparing starting models. 

Figure 2-1-6. Right-clicking on a bond, for example.

You can make changes to atoms, bonds or molecules directly in the workspace.

 

For example:

• Right-click on any atom in the workspace to change the atom to another atom, set a charge, change isotopes or properties and more
• Right-click on any bond in the workspace to change the bond order (this can be particularly useful for setting zero-order bonds, or so-called dative bonds)
• Also right-click on any bond to manually set lengths or rotate dihedrals

 

Additional universal tools are available in the 3D builder, which will be demonstrated in next section, Section 2.2

Figure 2-2-1. Creating an empty entry.

1. Right-click anywhere in an empty section of the workspace
2. Choose Create New Entry > Create Empty Entry
3. When prompted, input ppy for the Entry title and click the green check
   • A new entry is added to the entry list titled ppy
   • The entry is selected (the row is highlighted) and included (the blue circle is filled)
   • Nothing appears in the workspace

Figure 2-2-2. Sketching 2-phenylpyridine.

4. With the ppy entry selected and included, from the main menu, go to Edit > 2D Sketcher

 

The 2D sketcher functions like many standard 2D molecular drawing tools. For a complete overview of using the sketcher panel, see the 2D Sketcher Panel documentation.

 

5. Draw 2-phenylpyridine (see Figure)

 

Note: Use the green check () for a quick clean up of any drawings. Use the show more button () to see additional drawing tools.

 

Note: Many keyboard shortcuts are available within the 2D sketcher (e.g. input atoms by typing symbols)

Figure 2-2-3. 2-phenylpyridine in the workspace.

 

6. Click Save Changes
7. Close the 2D Sketcher
   • The 2D sketch has been converted into a 3D model in the workspace
   • The default display is wireframe

Figure 2-2-4. Updating style.

We can change the display to ball-and-stick akin to the earlier provided structures:

 

8. Select all of the atoms in the workspace (use the selection tools as before, or you can also use Shift+Click+Drag)
9. In the Toolbar, click on the Style palette
10. Choose the ball-and-stick option ()
    • The style is updated

 

It is important to note that this structure is not optimized. For introductory concepts regarding quantum mechanical geometry optimizations, the following tutorials are recommended:

• Introduction to Geometry Optimizations, Functionals and Basis Sets
• Introduction to Multistage Quantum Mechanical Workflows

Figure 2-2-5. Opening the 3D Builder.

A structure can be modified in many ways. For example, you could reopen the 2D Sketcher and change this entry or create a new entry using the phenylpyridine molecule as a starting point. In addition, there are tools for working in 3D. Let’s briefly explore the latter.

 

11. In the Toolbar, click on the Build palette
    • The 3D Builder appears in the workspace

 

The 3D sketcher functions like many standard 3D molecular drawing tools. For a complete overview of using the sketcher panel, see the 3D Sketcher Panel documentation.

Figure 2-2-6. Selecting the H atom to be replaced.

Let’s suppose we wanted to add another phenyl ring adjacent to the nitrogen atom.

12. Select the H atom to be replaced

 

Figure 2-2-7. Adding a fragment.

13. In the 3D Builder, click Add Fragments and choose the benzene ring
    • The H atom is replaced with a phenyl group (the figure shows the workspace result after choosing the benzene ring)

 

 

Note: In the preferences menu, global settings for ‘Builder Behavior’ can be defined, including hydrogen adjustments.

Figure 2-2-8. A force field minimization.

We may wish to improve the initial geometry of the structure by using a force field minimization.

14. Select all of the atoms in the molecule
15. Click the Minimize Selected Atoms
    () button in the 3D Builder

 

Note: A force field is used to minimize the geometry (OPLS4). Keep in mind that this will be done at a lower level of accuracy compared to quantum mechanical geometry optimizations. Also note that metal atoms are generally not parameterized for force field minimization.

Figure 2-3-1. Using the Single Complex Panel.

1. Go to Tasks (top right of the toolbar) > Materials > Structure Builders > Single Complex
   • The Build Single Complex panel opens
   • We will cover the Tasks Menu in more detail in Section 3

 

Note: All panels include a button to directly access Help documentation in the bottom right corner ().

 

Let’s prepare a starting model for Ir(acac)₃.

2. Retain the Define complex section as is: Ir as the central atom with an octahedral, nuclearity as monomeric, and facial geometry. Skip the Ligands section, we will return to it shortly
3. In the Specify ligands section, Ligand sketcher section of the panel, click on the first row. Click the Template dropdown menu (). Find and click acetylacetonato (acac).
   • Click the pencil icon next to the dropdown menu to see the acac ligand in the 2D sketcher. R1 and R2 used to denote attachment points to a metal center
   • In the 2D sketcher you draw your own ligands, save templates, and set your own attachment points.

Figure 2-3-2. Updating the ligand counts.

4. Increase Copies to 3
   • This indicates that we want three acac ligands in total, which will satisfy the coordination of the Ir center
5. Click Create
6. Close the Build Single Complex panel

Figure 2-3-3. Ir(acac)₃ in the workspace.

A new entry has been added to the entry list titled Ir-complex containing an Ir(acac)₃ molecule. It is selected and included by default. Feel free to stylize the molecule as we have before, rename as you wish and use the mouse actions to visualize the complex.

 

Note again that this structure is not optimized at a quantum mechanical level. For tutorials related to optimizations, see:

• Introduction to Geometry Optimizations, Functionals and Basis Sets
• Introduction to Multistage Quantum Mechanical Workflows

Figure 2-4-1. Defining the monomer.

1. Go to Tasks (top right of the toolbar) > Materials > Structure Builders > Polymer
   • The Polymer Builder panel opens
   • We will cover the Tasks Menu in more detail in Section 3

 

Note: All panels include a button to directly access Help documentation in the bottom right corner ().

 

The settings on the Groups tab can be changed to produce a wide variety of polymer models.

2. Maintain the Monomer type as All-atom and the Initiator and Terminator as H
3. In the Monomers section, switch the dropdown menu from Custom to vinyl chloride
   • Additional monomers can be defined to create copolymers
   • Custom monomers can be sketched with the 2D sketcher

Figure 2-4-2. Composition tab.

4. Go to the Composition tab
5. Retain the Homopolymer selection with 10 for the Number of monomers
   • Vinyl chloride is indicated as the monomer
   • Each polymer unit will be composed of 10 monomers

 

Note: If you were to run the job at this point, you would build one 10-mer unit, which could then be used as a component of a Disordered System (see Section 2.5). However, because we wish to model a homopolymer, we can produce a periodic cell directly using the amorphous cell tab.

Figure 2-4-3. Amorphous cell tab.

6. Go to the Amorphous Cell tab
7. Check Create amorphous cell
8. For Dihedral angle distribution, choose Boltzmann at 300.00 K
   • The polymers will grow simultaneously in the cell via self-avoiding random walk
9. For Number of polymers, input 25
   • The Total atoms dialog at the bottom of the panel indicates the number of atoms in each polymer unit. Thus, this job will create a box with 1550 atoms (62 atoms * 25 polymers)
10. Retain the remaining default settings
11. Change the Job name to polymer_builder_PVC

 

For a complete description of the extensive capabilities of the Polymer Builder panel, see the associated help documentation.

Figure 2-4-4. Amorphous cell tab.

This job will be nearly instantaneous, but this builder is our first example where we will perform a calculation. The computational setup required for this is discussed below:

 

To adjust job settings, you can always click on the gear () button next to the Job name.

 

12. Make sure that you have a CPU host set to run this job (a localhost will be sufficient)
    • If you have no available hosts, see the help documentation
13. Click Run (either in the Job Settings panel or in the Polymer Builder panel)

 

Note: Your Host may not match that which is shown in the Figure. For a complete discussion of the Job Settings Dialog Box, see the help documentation.

Figure 2-4-5. The amorphous polyvinyl chloride output.

14. Close the Polymer Builder panel

 

You will notice that the job has started, because the Job Monitor (top-right corner of the toolbar) will turn green: . We will discuss the Job Monitor in more detail in Section 3.2

 

When the job is complete, a new entry group will be incorporated titled MD: polymer_builder_PVC_system (1) containing one entry titled amorphous poly(vinyl chloride)

15. Includethe entry is represented in the Workspace, the circle in the In column is blue. the amorphous poly(vinyl chloride) entry
    • The box is visible in the workspace

 

Note, that this system is just a starting model. It has not been equilibrated by molecular dynamics (MD).

Figure 2-5-1. Water component after drawing.

To use the Disordered System Builder, you should first prepare separate entries for each component of your system:

1. Following similar steps from Section 2.2, prepare an entry for water

Figure 2-5-2. PEG component after polymer building.

2. Following similar steps from Section 2.4, prepare an entry containing a single 10-mer of polyethylene glycol (monomer = oxyethylene)
   • Note that to prepare just a 10-mer and not an amorphous cell, you should build the polymer without checking Create amorphous cell in the polymer builder panel
   • On the Chain Growth tab, choose Random for the Backbone dihedral to produce a 10-mer that is not completely linear

 

If you are having trouble preparing the starting entries, feel free to import Section_02 > disordered_system_components.mae from the provided tutorial files:

 

Figure 2-5-3. The entries associated with the two components, selected in the entry list.

3. After drawing/building or importing, 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 two entries from the entry list
   • Recall that selection means to highlight both entries
   • When using the Disordered System Builder, always 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 components from the entry list (if using a substrate, it is recommended to includethe entry is represented in the Workspace, the circle in the In column is blue. the substrate)

Figure 2-5-4. The Disordered System Builder.

4. Go to Tasks > Materials > Structure Builders > Disordered System
   • The Disordered System Builder panel opens
   • The two selected components are by default loaded into the panel

Figure 2-5-5. Setting the components

We are going to build a box that is ~40 wt% PEG.

5. For Initial state, choose Tangled chain
   • Visit the documentation for the differences between the choices. Typically, tangled chain allows for the quickest build
6. Change Number of molecules to 1500
   • Although we will not provide steps for running MD in this tutorial, here we are building a box that is a reasonable size if you do wish to proceed to a MD Multistage Workflow on your own
7. In the Components table, change the Molecules for water to 1460 and PEG to 40
   • The wt% appears in the panel and the table updates interactively

 

Note: We will not utilize the Cells tab and the Disorder tab here, but you can use these tabs to generate multiple cells for sampling, or to create homogeneous disordered systems of the individual components at different initial packing densities

Figure 2-5-6. Setting the Disorder and running the job

8. Change the Job name to disordered_system_PEG_water

 

This job will take about 3 minutes on a CPU host. To adjust job settings, click on the gear () button next to the Job name.

 

9. Click Run
10. Close the Disordered System Builder
    • The panel interacts with the workspace in real-time. It is therefore important to always close it after use

Figure 2-5-7. Output of the Disordered System Builder in the workspace.

When the job is complete, a new entry group will be incorporated titled MD: disordered_system_PEG_water_system (1) containing one entry titled disordered_system_PEG_water_all_components_amorphous

11. Includethe entry is represented in the Workspace, the circle in the In column is blue. the new entry
    • The box is visible in the workspace
    • The components are colored by default, but feel free to stylize as you wish

 

Note that this system is just a starting model. It has not been equilibrated by molecular dynamics (MD). For more on building disordered systems, and for the detailed steps for running MD on this specific system, see the Disordered System Building and MD Multistage Workflows tutorial

Figure 2-6-1. Importing a .cif file.

1. From the main menu, go to File > Import Structures
   • The Import panel opens
2. Navigate to the working directorythe location where files are saved. where you downloaded the tutorial files, and choose Section_02 > ZrO2.cif
3. Click Open
   • A new entry is loaded into the workspace

 

Note: Only the symmetrically unique atoms will be displayed at first. See below for building a cell from these unique atoms.

Figure 2-6-2. Renaming and styling.

4. Rename the entry to c-ZrO2 (as mentioned before, by double-clicking on the current name in the entry list)
5. Click on Presets in the Toolbar and select Ball and Stick
   • The style of the Zr and O atom changes in the workspace

Figure 2-6-4. Show Periodic Structure Tool.

6. Click on Show Periodic Structure Tool Window in the bottom right corner of the interface
7. Click Build Cell
8. Select Translate to First Unit Cell, Recalculate Connectivity, Recalculate Bond Orders and set the Extents to 1 in every direction.

Figure 2-6-5. Extended view of the crystal.

9. Click Apply
   • An extended view of the crystal is displayed in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed.
   • Cell 3 x 3 x 3 is shown in green in the bottom right  

Note: The specified extents are only for visualization; we have not changed anything about the crystal structure or its periodic boundary conditions.

Figure 2-6-6. Create a P1 symmetric supercell.

10. Click on Show Periodic Structure Tool Window on the bottom right corner of the interface again
11. Select Make P1 Cell
    • A new entry is added to the entry list named c-ZrO2 P1 and is includedthe entry is represented in the Workspace, the circle in the In column is blue.
    • The light blue square expands around the supercell, as the dimensions of the cell have changed

Note: More sophisticated transformations can be done through Tasks > Materials > Tools > Redefine Lattice

Figure 2-6-7. Revert to Asymmetric Unit (ASU).

12. Includethe entry is represented in the Workspace, the circle in the In column is blue. the entry c-ZrO₂ in the workspace only (the original entry)
13. Click on Show Periodic Structure Tool Window on the bottom right corner of the Maestro Interface again
14. Click Revert to ASU
    • The supercell reverts to the asymmetric unit

 

Note that these structures are not yet optimized at the quantum mechanical level. To proceed to study these structures, one should next perform an appropriate optimization.

Figure 3-1-1. Materials task menus.

Under Tasks > Materials, you will find the main six branches of available panels: Structure Builders, Enumeration, Quantum Mechanics, Classical Mechanics, Informatics and Tools.

 

The list of panels below Browse All are recently visited panels. Your list may be different from the one shown in the figure.

 

The tasks menu also has a built-in search function, which can be used to find panels by keywords.

Figure 3-1-2. Favoriting.

If there are some panels which you use frequently, you can save them to your Toolbar to avoid having to access them from the Tasks menu repeatedly. Simply click the Star that appears next to any panel name in the tasks menu, and that panel will then appear in your Favorites Toolbar in all future MS Maestro sessions.

Figure 3-2-1. Job monitor.

 

Clicking on the icon, you will see a list of current and past jobs, as well as their statuses.

 

Use the Monitor button to access more detailed information about your jobs. From this panel, you can also, for example:

• Track .log or other files in real-time
• Kill jobs as needed
• Generate postmortem files to send to support

Figure 3-3-1. A Workflow Action Menu (WAM) button in the entry list.

Because we prepared an amorphous cell in the polymer builder section above (Section 2.4), the MS Maestro interface proposes that you may be interested in next performing an MD Multistage Workflow. A similar proposal is present for the box prepared in Section 2.5. The Workflow Action Menu (WAM) button in the entry list can be used for direct access to this subsequent panel. WAM buttons are useful for answering the “What can I do next?” question.

Figure 3-4-1. An example of a Results panel.

Many workflows utilize specialized Results panels for viewing outputs of calculations or simulations. For example, after running an optoelectronics job using the Optoelectronics Calculations panel, the output can be easily analyzed in the Optoelectronics Results panel, accessed via the Tasks menu.

 

Typically, if a workflow has a Results panel associated with it, the output will also include a WAM Button (see Section 3.3)

Figure 3-5-1. The Project Table icon.

1. Open the Project Table by clicking on the Table icon in the top right corner of the toolbar

Figure 3-5-2. The Project Table.

Depending on which operations and calculations you have done so far in the tutorial, you will see details associated with the various entries.

 

For example, the organometallic complexes were “cleaned-up” using a force field during building and thus have a Potential Energy property. Likewise, the periodic systems have information about the unit cells, as well as volume and density properties.

 

Of course, when more complex calculations are run, properties will be displayed accordingly.

Figure 3-5-3. Opening Property Tree

Right click on any property for access to additional functionality, including Hide, Sorting, Coloring and more.

 

Use the Property Tree () to show or hide properties in the table.

 

 

 

For a complete summary of 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. panel, see the help documentation.