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/builders_polymer_polymer_interface.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 polymerpolymer_tutorial, click Save
   • The project is now named polymerpolymer_tutorial.prj

Figure 3-1. Setting the monomer to styrene.

1. Go to Tasks > Materials > Structure Builders > Polymer
   • The Polymer Builder panel opens

First we’ll build an isotactic 30mer homopolymer of polystyrene (a linear polymer composed of 30 styrene monomers)

2. In the Groups tab:
   • under Monomers, from the Custom dropdown menu, select styrene
3. Click on the Composition tab

Figure 3-2. Define composition.

4. Set the number of monomers to 30
5. Click on the Chain Growth tab

Figure 3-3. Parameterize the chain growth and run.

6. For Backbone dihedral, select Random
7. For Affected dihedrals, select All
8. Change the Job name to polymer_builder_styrene
9. Adjust the job settings () as needed
   • This job requires a CPU host and can be . The job can be completed in a couple of minutes.
   • If you would like to run the job, click Run. Otherwise, pre-generated results are provided
10. If you’d like to import the structure rather than run the job, import Section_03 > polymer_builder_styrene-polymer.maegz from the tutorial files (via File > Import Structures).

Figure 3-4. Polystyrene in the workspace.

Once the job is complete, an isotactic 30mer homopolymer of polystyrene can be viewed in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

Note: Due to the random dihedral angles the generated structure will look different than the one pictured in the Figure.

Figure 3-5. Build the second polymer.

Keep the Polymer Builder panel open and we will repeat the process for polyvinyl chloride, which will be the second polymer in the system.

11. Return to the Groups tab:
    • under Monomers, from the Custom dropdown menu, select vinyl_chloride
12. Change the Job name to polymer_builder_vinylchloride

Note that all of the other settings in the composition and chain growth tabs are maintained, so we will again be building a 30mer.

13. If you’d like to import the structure rather than run the job, import Section_03 > polymer_builder_vinylchloride-polymer.maegz from the tutorial files (via File > Import Structures). Otherwise, to run the job, click Run.
    • The job should complete within a few minutes
14. Close the Polymer Builder panel

Figure 3-6. Polyvinyl chloride in the workspace.

You should now have two entries in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion corresponding with the polystyrene and polyvinyl chloride 30mers. We will use these in Section 5.

Figure 4-1. Setting the parameters in the nanostructure builder panel.

1. Go to Tasks > Materials > Structure Builders > Nanostructures
   • The Nanostructure Builder panel opens
2. For Termination, keep Periodic selected
   • This generates an infinite sheet as opposed to a capped finite plane
3. For Dimensions (unit cells), input 12 x 12
   • This is the quantity of graphene unit cell translations in the a and b directions that will comprise the new P1 cell
4. For Number of bilayers, input 2
5. Change the Job name to layered_graphene
6. If you’d like to import the structure rather than run the job, import layered_graphene.maegz from the tutorial files (via File > Import Structures). Otherwise, to run the job, click Run
   • The job should complete within a few minutes
7. Close the Nanostructure Builder panel

Figure 5-1. Selecting and including for the build.

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 poly(styrene) and includethe entry is represented in the Workspace, the circle in the In column is blue nanosheet
   • Recall that 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 means to highlight from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and includethe entry is represented in the Workspace, the circle in the In column is blue means to fill the blue circle to view the entry in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed

Note: Please refer to the Glossary of Terms for the difference between includedthe entry is represented in the Workspace, the circle in the In column is blue 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.

Figure 5-2. Disordered System Builder panel.

2. Go to Tasks > Materials > Structure Builders > Disordered System
   • The Disordered System Builder panel opens
   • poly(styrene) should appear as the only component, otherwise, go back to Step 1 and ensure that the polymer is 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 5-3. Set number of molecules and import substrate.

3. Select Tangled chain for the Initial state
4. Change the Number of molecules to 20
   • This will generate 20 molecules of the polystyrene 30mer in our system
5. Check Substrate
6. Click Import
   • nanosheet should appear next to the import button
   • If it does not import, ensure that nanosheet was includedthe entry is represented in the Workspace, the circle in the In column is blue in Step 1 of this section

Figure 5-4. Define Interface.

7. Change the Substrate type to Planar interface
8. Click Define Interface
   • The Define Interface panel opens
   • A plane appears in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed indicating where the build will occur. We want to build up in the c direction, as indicated
9. In the Define Interface panel, set both buffers to 2 Å
   • This will aid the build and will be reconciled in the later MD stages
10. Click OK

Note: The c (or z) direction is preferred for the crystal vector, particularly if subsequent steps will involve MD simulations as they do here.

Figure 5-5. Select PBC and name the build.

11. For Periodic Boundary Conditions (PBC), select Use/expand substrate PBC from the dropdown
12. Change the Job name to disordered_system_firstpolymer
13. Go to the Disorder tab

Note: In this tutorial, we do not use the Cells tab, but in practice, if you wanted to sample many builds, you could do so there.

Figure 5-6. Parameterize the disordered build.

14. Set the Initial density to 0.9
15. Select Color molecules by component
16. Click the Disorder Options button
17. Change the Dihedral angle distribution to Boltzmann
18. Click OK
    • This job requires a CPU host. The job can be completed in about 15 minutes on a CPU host
19. If you’d like to import the output rather than run the job, close the panel and import Section_05 > disordered_system_firstpolymer_system-out.cms from the tutorial files (via File > Import Structures). Otherwise, click Run and then close the Disordered System Builder.
    • The job should complete within 10 minutes  

Note: The initial density of 0.9 was chosen because of the persistence length of this polymer. For more rigid polymers, you may need to reduce the density to a much lower value (e.g. 0.3) to facilitate efficient building.

Figure 5-7. Output of the disordered build.

Once the build is complete, the output will be incorporated into the workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

Note: The unit cell display may be staggered, but this is only a visual matter and can be ignored. While this is purely visual, we can make an adjustment to realign the box if we wish using the Manipulate Cell tool

Figure 5-8. Setting the MD Multistage Workflow.

Now that we have prepared the disordered system. We will use an MD protocol to relax the polymer chains.

20. 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 and includethe entry is represented in the Workspace, the circle in the In column is blue the output: disordered_system_firstpolymer_all_components_amorphous
21. Go to Tasks > Materials > Classical Mechanics > MD Simulations > MD Multistage Workflow
    • The MD Multistage Workflow panel opens
22. Check Relaxation protocol and keep the Materials relaxation as default
    • This protocol includes three stages
23. For the fourth stage, select Molecular Dynamics from the dropdown menu
24. Change the total Simulation time (ns) to 5
25. Click Advanced Options

Figure 5-9. Adjusting the coupling style.

26. Set the Coupling style to Semi-isotropic
27. Click OK

Note: Setting the coupling style to semi-isotropic will scale the a and b dimensions uniformly, while the c dimension changes independently.  The Constant area coupling style can be used to maintain the a and b dimensions while applying the pressure tensor along c. See the documentation on the Advanced Options dialog box for more information.

Figure 5-10. Naming and running the job.

28. Set the Job name to multistage_simulation_firstpolymer
29. Adjust the job settings () as needed
    • This job requires a GPU host. The job can be completed in about 30 minutes.
    • If you would like to run the job, click Run. Otherwise, pre-generated results are provided
    • 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
30. Close the MD Multistage Workflow panel

Figure 5-11. Output of the MD job.

The polystyrene is packed atop the graphene.

(if you are importing the structure rather than running the job, you will do so in Section 6)

Figure 6-1. Importing the pre-generated file.

1. If you ran the job in Section 5, skip to Step 5.
2. Otherwise, go to File > Import Structures
3. Navigate to where you downloaded the tutorial files and choose the Section_06 > multistage_simulation_firstpolymer-out.cms file.
4. Click Open

Note: If using the pre-generated file, the trajectory data is not provided because it is not necessary to proceed. You can safely click on either Remove Data or Cancel if the Missing Trajectory dialog pops up.

Figure 6-2. Selecting and deleting graphene.

During the simulation, one or more graphene layers may have shifted across the periodic boundaries to the top of the cell. If not, proceed to Step 8. If so, follow the next steps to erase any graphene above the polystyrene to prepare for the next polymer:

5. Set your selection scope to molecules using the selection scope dropdown menu or by typing M on your keyboard.
6. Select any graphene molecules above the polystyrene
7. Go to the Build menu in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed and click Delete selected atoms.
   • The graphene layer is removed

Figure 6-3. Top of the box with no graphene.

The top of your box should just be a polymer layer.

Figure 6-4. Selecting and including for the build.

We are now ready to essentially repeat the general steps of Section 5 on top of the first polymer.

8. 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 poly(vinyl chloride) while keeping the output from the MD (without any graphene above the polystyrene) 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

Figure 6-5. Disordered system builder panel.

9. Go to Tasks > Materials > Structure Builders > Disordered System
   • The Disordered System Builder panel opens
   • poly(vinyl chloride) should appear as the only component
10. Verify that all of the settings used for Section 5 still apply
11. Click Import
    • disordered_system_firs... should appear next to the import button
12. Keep the Substrate type: as Planar interface
13. Click Define interface
    • The Define interface panel opens

Figure 6-6. Define interface.

14. Make sure that the Crystal vector is set to c
    • The plane appears in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed indicating where the build will occur. It may not default correctly. We want to build up in the c direction again
15. The previous settings are otherwise okay. Click OK

Figure 6-7. Running the job.

16. Change the Job name to disordered_system_secondpolymer

Again, all of the settings from Section 5 can be used here, so no need to adjust the parameters.

17. If you’d like to import the output rather than run, close the panel and import Section_06 > disordered_system_secondpolymer_system-out.cms from the tutorial files (via File > Import Structures). Otherwise, click Run and then close the Disordered System Builder
    • You may be warned about periodic bonds in the c direction. You can dismiss this warning with Continue. So long as the final system has 40 + n molecules where n is the number of graphene sheets, there were no issues.
    • The job should complete within 5 minutes

Note: It is a best practice to close the Disordered System Builder whenever you are done using it, particularly if your project includes large systems.

Figure 6-8. Output of the disordered build.

Once the build is complete, the output will be incorporated.

If any graphene layers shift again, be sure to follow the above steps to remove the layer.

Note: The unit cell display may be staggered, but this is only a visual matter and can be ignored. While this is purely visual, we can make an adjustment to realign the box if we wish using the Manipulate Cell tool

Figure 6-9. Removing the fourth stage.

We will run an MD protocol again to relax the system now with all of the components.

18. 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 and includethe entry is represented in the Workspace, the circle in the In column is blue the output: disordered_system_secondpolymer_all_components_amorphous
19. Go to Tasks > Materials > Classical Mechanics > MD Simulations > MD Multistage Workflow
    • The MD Multistage Workflow panel opens
20. Check Relaxation protocol and keep the Materials relaxation as default (these settings should be maintained from our previous use of this panel)
    • This protocol includes three stages
21. Remove the fourth stage ()

Figure 6-10. The MD Multistage panel before job submission.

22. Set the Job name to multistage_simulation_secondpolymer
23. Confirm that the job will run on a GPU host by checking the run settings (). This job takes ~5 minutes on a GPU host. If you would prefer to continue with pre-generated files, proceed to the next section without running the job. Otherwise, click Run
24. Close the MD Multistage Workflow panel

Figure 7-1. Importing the pre-generated file.

1. If you ran the job in Section 6, skip to Step 5
2. Otherwise, go to File > Import Structures
3. Navigate to where you downloaded the tutorial files and choose the Section_07 > multistage_simulation_secondpolymer-out.cms file
4. Click Open

Figure 7-2. The output from the second MD job.

During the simulation, one or some of a graphene layer may have shifted again within the periodic boundary conditions. Feel free to erase one or more sheets if you wish following the steps outlined in Section 6. In practice, there will be situations where you want to keep at least one sheet and situations where you wish to remove all of the graphene. One graphene sheet was deleted in the system.

Figure 7-3. Analyzing the density profile.

Let’s analyze the density profile of the system. Note that polystyrene has a known density of ~1.05 g/cm³ and polyvinyl chloride has a density of ~1.38 g/cm³.

5. Includethe entry is represented in the Workspace, the circle in the In column is blue the full system in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed: disordered_system_secondpolymer_all_components_amorphous
6. Go to Tasks > Materials > Tools > Density Profile
   • The Density Profile panel opens
7. Click Analyze Workspace
   • Data is loaded into the panel
8. Change the Axis to Z-Axis and ensure that you are on the Profile tab
   • The graph shows the density of the system as a function of the Z-Axis Depth (or more simply, as a function of box height)
   • The density in the graphene layers spikes because of the sheets and gaps, whereas the density in the polystyrene and polyvinyl chloride layers is reasonably close to the experimental densities. In general, longer simulation would be necessary to get within 2-3% of the experimental density for each layer.

Figure 7-4. Analyzing the cross section density profile.

We can also use the Cross Section tool to look at the molecular features of the interfacial layer.

9. Change to the Cross Section tab
10. Use the arrows or the layer input box to control the plane that now appears in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed. Shift the plane to approximately where the two polymers meet.
    • In the provided output, it is approximately layer 76

Feel free to explore other cross sections in the box by navigating with the arrows.

Figure 7-5. Analyzing atoms at a specific location from the cross section density profile.

Finally, note that the cross density tool can be used to directly interact with the workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

11. With the layer aligned near the polymer-polymer interface, click anywhere within the cross section density plot to visualize the atoms at that location
12. Click Re-display All Atoms to visualize the full system again

Feel free to explore the topology at the interface further.

Depending on your research direction, you may now proceed in several directions to study this polymer-polymer interface.