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 files are included for running jobs or examining output. Download the zip file here: schrodinger.com/sites/default/files/s3/release/current/Tutorials/zip/surface_tension.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 surface_tension_tutorial, click Save
   • The project is now named surface_tension_tutorial.prj

Figure 2-3. Importing the starting molecules.

8. Go to File > Import Structures
9. Navigate to where you downloaded the tutorial files (presumably your working directory) and choose input_molecules.mae from the provided files
10. Click Open
    • A new entry 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 containing three molecules
    • If you would prefer to practice drawing these molecules on your own with the 2D Sketcher, feel free to do so (for practice using the 2D Sketcher, see the Introduction to Maestro for Materials Science tutorial)

Figure 3-1. Selecting all three entries and opening the Disordered System Builder.

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 all three entries from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
2. Go to Tasks > Materials > Structure Builders > Disordered System
   • The Disordered System Builder panel opens

Note: For general practice with the Disordered System Builder, see the Disordered System Building and MD Multistage Workflows tutorial

Figure 3-2. Setting the Components parameters.

The Disordered System Builder is typically used to create an amorphous cell containing multiple components. Instead, here we wish to prepare homogeneous cells, four for each component. To do so:

3. For Initial state, select Tangled chain
4. Change the Number of molecules to 343
   • This will be total number of molecules in each cell
5. Change the DME number of Molecules to 115
   • This is not actually relevant for our build, but the panel will not run unless the molecules sum to the expected total
   • Otherwise, pay no attention to the Components table. We are going to obviate that momentarily
6. Go to the Cells tab

Figure 3-3. Setting the Cells parameters.

7. Uncheck All components
   • This avoids the construction of the mixed cell
8. Check Homogeneous cell of each component
   • This instructs the builder to prepare the homogeneous cells instead
9. Change Number of cells of each type to 4

Figure 3-4. Setting the Disorder parameters and running the job.

10. Change the Job name to disordered_system_DME_ACN_FA
11. This job takes ~5-10 minutes on a CPU Host. If you would like to run the job yourself, adjust your Job settings () as needed and click Run.

If you would prefer to proceed with pre-generated structures, you can import the amorphous cells via File > Import Structures. Navigate to where you downloaded the tutorial files and choose the Section_03 > disordered_system_DME_ACN_FA > disordered_system_DME_ACN_FA_componentn_m_system-out.cms files.

12. Close the Disordered System Builder panel

Figure 3-5. Visualizing the output.

Feel free to visualize or stylize any of the output cells.

Figure 3-6. Selecting the entries and opening the MD Multistage Workflow panel.

We will proceed to run an MD protocol to densify the systems before proceeding to expand the cells and prepare the slabs.

13. 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 twelve new entries from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion (Shift + Click on all 12 rows)
14. Go to Tasks > Materials > Classical Mechanics > MD Simulations > MD Multistage Workflow
    • The MD Multistage Workflow panel opens

Figure 3-7. Setting up the MD Multistage Workflow panel.

15. Ensure that Use structures from directs to the 12 entries from above
16. Check the box for Relaxation protocol and choose Compressive from the dropdown menu
17. Click the button to remove the 8th stage

Figure 3-8. Naming and running the job.

18. Change the Job name to multistage_simulation_DME_ACN_FA
19. This job takes several hours on a GPU Host. If you would like to run the job yourself, adjust your Job settings () as needed and click Run.

If you would prefer to proceed with pre-generated structures, you can import the amorphous cells via File > Import Structures. Navigate to where you downloaded the tutorial files and choose the twelve multistage_simulation_DME_ACN_FA_00n-out.cms files in the Section_03 > multistage_simulation_DME_ACN_FA > multistage_simulation_DME_ACN_FA_00ndirectory

Note: MD simulations have a number of files associated with the job, for a full description of each file type see the help documentation on Desmond Files

20. Close the MD Multistage Workflow panel

Figure 3-9. Output of the equilibration.

When the job finishes or after importing, twelve new entries are added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion. The systems have been densified and we are now ready to expand to a larger cell and then generate a slab.

Figure 3-10. Using the Extents tool.

21. Includethe entry is represented in the Workspace, the circle in the In column is blue the first of the twelve compressed entries in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
22. Click on the button to open the Periodic Structure Tool Window
23. Go to Build Cell
24. Click Extents
25. Insert 1 for the +A, +B and +C directions
26. Click Apply
    • Click Continue if prompted with a warning
    • An extended view of the periodic cell is displayed in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
    • Cell 2 x 2 x 2 is shown in green in the bottom right

If you are not familiar with Periodic Cells and their manipulation in MS Maestro, visit the Building and Manipulating Crystal Structures tutorial

Figure 3-11. Extended view of the cell.

The extended view of the cell is shown in the figure. This extent expansion is purely visual. In order to generate a new cell of this size, we will need to use the Make P1 Cell option.

Figure 3-12. The new, renamed cell.

27. Click on the button to open the Periodic Structure Tool Window
28. Choose Make P1 Cell
    • A new entry is added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
29. Rename the entry DME_largecell_1

Figure 3-13. The twelve new, renamed cells.

30. Repeat the above steps for the remaining eleven cells. Note that you can include all eleven simultaneously in the workspace and perform the periodic operations synchronously
    • Alternatively, simply import Section_03 > largecells_all.mae from the provided files and proceed with these outputs
31. Rename the entries DME_largecell_n, ACN_largecell_n and FA_largecell_n where n = 1, 2, 3, etc.

Your entry list should match that which is shown in the Figure (in no particular order), and you should now have 12 cells, four for each component, each with ~15,000-25,000 atoms. 

Figure 3-14. Including a cell, opening the panel and loading in the structure.

For surface tension, we need an interface which can either be one phase and vacuum or one and another non-vacuum phase (also known as the interfacial tension). Here, we are interested in a single phase surface tension, so we will need to introduce a vacuum layer above our cell. We can do so by generating a slab for each of the entries. We will detail the steps for one entry, and then it can be repeated for all, or you can import pregenerated slabs.

32. Includethe entry is represented in the Workspace, the circle in the In column is blue DME_largecell_1in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
33. Go to Tasks > Materials > Structure Builders > Slabs and Interfaces
    • The Build Slabs and Interfaces panel opens
34. Click Load
    • DME_largecell_1 appears in the panel
35. Check Define slab

Figure 3-15. Naming and running the job.

We can maintain all of the defaults, which will generate a slab with a ~100 Å vacuum buffer. A cell size of ~75 Å x 75 Å x 75 Å with a ~100 Å buffer is a reasonable default for the upcoming surface tension jobs. If you are interested in learning more about this tool, visit the help documentation or see the Modeling Surfaces tutorial.

36. Change the Job name to surfaces_interfaces_DME_largecell_1

This job takes several minutes on a CPU Host. If you would like to run the job yourself, adjust your Job settings () as needed and click Run. If running the job, you will have to click Continue to a warning about the cell size. Repeat these steps for the remaining eleven cells. Or, if you would prefer to proceed with pre-generated structures, you can import all twelve slabs via File > Import Structures. Navigate to where you downloaded the tutorial files and choose the Section_03 > slabs_all.mae file

37. Close the Build Slabs and Interfaces panel

Figure 3-16. The twelve slabs.

After running the jobs or importing, you should have twelve slabs in your entry list that are nearly ready for surface tension calculations.

Figure 3-17. Prepare for MD. 

As a final step, the slabs tool generates cells that are not ready for Desmond simulations. The Prepare for MD panel is used for cleaning up bond orders, selecting a force field, and creating a simulation box that is Desmond ready:

38. 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 twelve slabs in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
39. Go to Tasks > Materials > Classical Mechanics > MD Simulations > Prepare for Molecular Dynamics
    • The Prepare for MD panel opens
40. Change the Job name to md_prep_all_slabs
41. This job takes several minutes on a CPU Host. If you would like to run the job yourself, adjust your Job settings () as needed and click Run. Or, if you would prefer to proceed with pre-generated structures, you can import the prepared slabs via File > Import Structures. Navigate to where you downloaded the tutorial files and choose the four files in the Section_03 > md_prep_all_slabs > ACN_largecell_n_001-surface_system-out.cms where n=1-4 directory. Repeat for DME and FA. There will be 12 files total.

Figure 3-18. The twelve slabs after prep for MD.

After running the jobs or importing, you should have twelve slabs in your entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion that are now completely ready for surface tension calculations.

Figure 4-1. Selecting the entries and opening the Surface Tension Calculation panel

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 all twelve slabs in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
2. Go to Tasks > Materials > Classical Mechanics > Surface Tension > Surface Tension Calculations
   • The Surface Tension Calculation panel opens

Figure 4-2. Setting up the Surface Tension Calculation.

3. In the Simulation protocols section, check Add relaxation step
4. Increase the Simulation time to 1000 ps
5. Increase the Trajectory recording interval to 20 ps
6. Change the Job name to surface_tension_DME_ACN_FA

This job takes about 20 minutes per cell per GPU on a GPU Host. If you would like to run the job yourself, adjust your Job settings () as needed and click Run. Or, if you would prefer to proceed with pre-generated structures, you can import the twelve surface_tension_DME_ACN_FA-00n-out.cms files in the Section_04 directory from the provided tutorial files for the analysis steps. Note that the files are all in separate directories because there are file dependencies within each directory.

If you run the job, a warning will appear regarding running over 10 jobs with this panel. Click OK.

7. Close the Surface Tension Calculation panel

Figure 4-3. The outputs in the entry list.

After running the jobs or importing, you should have twelve new entries in your entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion corresponding with each cell.

Note that some drifting may occur relative to the unit cell in the workspace, but this is purely visual. If you like, you can use the button to open the Periodic Structure Tool Window and Translate to First Unit Cell.

Figure 4-4. Accessing the Surface Tension Results panel via the WAM button.

We can analyze the outputs in two ways, with the Density Profile Viewer as well as with the Surface Tension Results panel. Let’s begin with the latter:

8. Use the WAM (workflow action menu) button () to open the Surface Tension Viewer panel for any of the twelve outputs
   • Alternatively, access the panel via Tasks > Materials > Classical Mechanics > Surface Tension > Surface Tension Results

Figure 4-5. Surface Tension Viewer panel.

Here we are looking at an output from an acetonitrile run. You can use the blue sliders or the Time range input in the panel to adjust the range for extracting the surface tension.

The Average property reports the surface tension in dyne/cm. Note that an individual run has a large standard deviation for surface tension as a function of time. We recommend running multiple cells of each component so that we can average their means.

You can use the Property dropdown to look at any of the individual pressure tensors.

Feel free to explore the Viewer for any of the twelve entries.

Figure 4-6. The Density Profile for one of the formamide runs.

We can also analyze the Density Profile for ACN. We expect the more volatile DME to have a significantly different density profile than the less volatile formamide:

9. Includethe entry is represented in the Workspace, the circle in the In column is blue any of the twelve outputs in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
   • In the Figure, we include a formamide system
10. Go to Tasks > Materials > Tools > Density Profile
    • The Density Profile panel opens
11. Click Analyze Workspace
12. Change the Axis to Z-axis

The density as a function of the Z-Axis Depth in the cell is shown.

Feel free to explore the Density Profiles for any of the runs.