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/builders_semicrystalline_polymer.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 semicrystalline_polymer_tutorial, click Save
   • The project is now named semicrystalline_polymer_tutorial.prj

Figure 3-1. Opening the Semicrystalline Polymer Builder panel.

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

Figure 3-2. Setting up the Semicrystalline Polymer Builder panel for a low target crystallinity.

We will construct two polyethylene (PE) semicrystalline polymers with varying target crystallinity percentages.

2. Ensure Polyethylene (PE) is the selected Crystal
3. Increase the Replicate unit cell to 12 by 11 by 5
4. For Monomers per chain enter 20
5. For Number of chains enter 200
6. Change the Job name to semi_crystal_builder_PE_low
7. Adjust the job settings () as needed
   • This job requires a CPU host. The job can be completed in about 1 hour on a CPU host
8. If you would like to run the job, click Run. Otherwise, we will proceed with pre-generated results in the next step
9. Once the job is successfully completed, a new semi_crystal_builder_PE_low-out_system group, with a single entry titled Polyethylene (PE), 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 in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and 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

This structure contains a low target crystallinity of 32.46%.

Figure 3-3. Setting up the Semicrystalline Polymer Builder panel for a high target crystallinity.

For the second PE semicrystalline polymer let’s increase the target crystallinity. Feel free to reset the panel if you’d like using the arrow in the bottom left corner of the panel

10. Once again, ensure Polyethylene (PE) is the selected Crystal
11. Increase the Replicate unit cell to 12 by 12 by 12
12. Keep the Monomers per chain as 20
13. Keep the Number of chains as 200
14. Change the Job name to semi_crystal_builder_PE_high
15. Adjust the job settings () as needed
    • This job requires a CPU host. The job can be completed in about 1 hour on a CPU host
16. If you would like to run the job, click Run. Otherwise, we will proceed with pre-generated results in the next step
17. Once the job is successfully completed, a new semi_crystal_builder_PE_high-out_system group, with a single entry titled Polyethylene (PE), 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 in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and 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
18. Close the Semicrystalline Polymer Builder panel

This structure contains a high target crystallinity of 84.98%.

Figure 3-4. Viewing the semicrystalline structures.

Alternatively, you can import in both structures

19. Go to File > Import Structures, navigate to the provided tutorial files and Open Section_03 > semi_crystal_builder_PE_low > semi_crystal_builder_PE_low-out_system-out.cms and Section_03 > semi_crystal_builder_PE_high > semi_crystal_builder_PE_high-out_system-out.cms

Figure 3-5. Translating to the first unit cell.

Let’s view the systems in their unit cells to better see the distinction between the crystal and amorphous layers.

20. With one of the structures 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, open the Show periodic structure tool window in the bottom right corner
21. Click Build Cell
22. Select Translate to First Unit Cell
23. Click Apply
24. Repeat this process for the other system as well

Figure 4-1. Opening the MD Multistage Workflow 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 both the semi_crystal_builder_PE_low-out_system-out group and the  semi_crystal_builder_PE_high-out_system-out group from Section 3, go to Tasks > Materials > Classical Mechanics > MD Simulations > MD Multistage Workflow
   • The MD Multistage Workflow panel opens
   • Selecting both PE structures allows us to only setup the MD calculation once

For a comprehensive overview on the MD Multistage Workflow panel, see the help documentation or the Disordered System Building and Molecular Dynamics Multistage Workflows tutorial.

Figure 4-2. Setting up the MD workflow.

2. Ensure that Use structures from says Project Table (2 selected entries)
3. Check Relaxation protocol and select Semicrystal relaxation 1
   • This relaxation protocol is a custom protocol for semicrystalline polymers, see the help documentation for more details
4. In Stage 6, for Stage Type, choose Molecular Dynamics
   • Should voids appear in the equilibrated structure, modify the ensemble coupling style in Advanced Options to anisotropic, rather than the default isotropic. Although the semicrystal relaxation protocol includes approximately 5 ns of anisotropic barostat, this duration may be insufficient for certain systems.
5. For Simulation time (ns), set total to 20
6. For Approximate number of frames, set to 100
7. Click Append Stage
   • Stage 7 is added to the workflow
8. In Stage 7, for Stage Type, choose Analysis

Figure 4-3. Running the MD workflow.

9. For Job name, enter multistage_simulation_semicrystalline
10. Adjust the job settings () as needed
    • This job requires a GPU host. The job can be completed in 4 hours
11. If you would like to run the job, click Run. Otherwise, pre-generated results are provided to view the structure
12. Once the job is successfully completed, two new groups will appear in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion, with two entries titled MD: semi_crystal_builder_PE_low-out_system and MD: semi_crystal_builder_PE_high-out_system
13. Close the MD Multistage Workflow panel

Figure 4-4. Opening the MS MD Trajectory Analysis panel.

14. If importing the files instead, go to File > Import Structures, navigate to the provided tutorial files and Open Section_04 > multistage_simulation_semicrystalline > multistage_simulation_semicrystalline_001 > multistage_simulation_semicrystalline_001-out.cms and Section_04 > multistage_simulation_semicrystalline > multistage_simulation_semicrystalline_002 > multistage_simulation_semicrystalline_002-out.cms
    • 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
15. In the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion, 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 MD: semi_crystal_builder_PE_low-out_system
    • Feel free to stylize the structures as you wish. In the figure the structures have been translated to the first unit cell once again.
16. Go to Tasks > Materials > Classical Mechanics > Trajectory Analysis > MS MD Trajectory Analysis or use the Workflow Action Menu (WAM) button which appears next to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
    • The MS MD Trajectory Analysis panel opens

Figure 4-5. Loading the MD results.

17. Click Load from Workspace if the results do not automatically load
    • The Simulation Detail tab fills with information about the system
18. Click the Bulk Properties tab

Figure 4-6. Viewing the bulk properties.

19. In the drop-down menu above the first plot, select Density

Figure 4-7. Viewing the final 20% density.

We may be interested in analyzing parameters from a specific portion of the trajectory. If we want to ensure that we are only looking at the trajectory from when the polyethylene cell is equilibrated, we can customize the Trajectory Range. In this case, let’s look at the final 20% of the simulation. 

20. Next to Trajectory Range, Click Final 20%

We see that the average density over the last 20% is 0.85 g/cm³ for our low semicrystalline PE structure.

Note: The data can be extracted as a PDF Report, Plots and Data using the Generate Report option

Figure 4-8. Loading results from the workspace.

Let’s view the density for our high semicrystalline PE structure

21. Back in our entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion, 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 MD: semi_crystal_builder_PE_high-out_system
22. With the MS MD Trajectory Analysis panel still open, click Load from Workspace
    • The results from our second MD are loaded into the viewer

Figure 4-9. Viewing the density for our high crystallinity structure.

23. Following the steps above view the final 20% density for this structure

We see that the average density over the last 20% is 0.91 g/cm³ for our high semicrystalline PE structure.

24. Close the MS MD Trajectory Analysis panel

Figure 5-1. Opening the Trajectory Density Analysis 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 the MD: semi_crystal_builder_PE_low-out_system-out entry from Section 4, go to Tasks > Materials > Classical Mechanics > Trajectory Analysis > Trajectory Density Analysis
   • The Trajectory Density Analysis panel opens

Figure 5-2. Running the Trajectory Density Analysis panel for the low crystallinity system.

2. Click Load from Workspace
3. Click All to include all atoms for the density analysis
4. For Job name, enter trajectory_density_analysis_PE_low
5. Adjust the job settings () as needed
   • This job requires a CPU host. The job can be completed in 5 minutes
6. If you would like to run the job, click Run. Otherwise, pre-generated results are provided to view the structure
7. Once the job is successfully completed, a new group titled MD: semi_crystal_builder_PE_low-out_system, is now in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
   • Feel free to rename this structure

Figure 5-3. Running the Trajectory Density Analysis panel for the high crystallinity system.

8. Repeat these steps for the MD: semi_crystal_builder_PE_high-out_system-out entry
9. For Job name, enter trajectory_density_analysis_PE_high
10. Adjust the job settings () as needed
    • This job requires a CPU host. The job can be completed in 5 minutes
11. If you would like to run the job, click Run. Otherwise, pre-generated results are provided to view the structure
12. Once the job is successfully completed, a new group titled MD: semi_crystal_builder_PE_low-out_system, is now in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
    • Once again, feel free to rename this structure
13. Close the Trajectory Density Analysis panel

Figure 5-4. Opening the Trajectory Density Analysis Viewer panel via the WAM button.

25. If importing the files instead, go to File > Import Structures, navigate to the provided tutorial files and Open Section_05 > trajectory_density_analysis_PE_low > trajectory_density_analysis_PE_low-out.cms and Section_05 > trajectory_density_analysis_PE_high > trajectory_density_analysis_PE_high-out.cms
26. In the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion, 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 MD: semi_crystal_builder_PE_low-out_system
    • Feel free to stylize the structures as you wish. In the Figure, the structures have been translated to the first unit cell once again.
27. Go to Tasks > Materials > Classical Mechanics > Trajectory Analysis > Trajectory Density Analysis or use the Workflow Action Menu (WAM) button which appears next to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
    • The Trajectory Density Analysis Viewer panel opens

Figure 5-5. Viewing the 1D profile for our low crystallinity PE system.

This panel views 1D and 2D profiles of the averaged density from a trajectory. Let’s start with a 1D profile.

28. Select Z from the Axis drop down menu
29. Change the Frames to 80 so the last 20% of the run is plotted

Figure 5-6.Viewing the 2D profile for our low crystallinity PE system.

30. Click the Density Projection tab
31. Select XZ from the Planes drop down menu

Now we are viewing the 2D density profile. These plots can be customized and saved.

Repeat this process for the MD: semi_crystal_builder_PE_high-out_system entry and view the density below.

Figure 6-1. Building a PE crystal structure.

The Semicrystalline Polymer Builder panel can also be used to build a PE crystal structure

1. Go to Tasks > Materials > Structure Builders > Semicrystalline Polymer
   • The Semicrystalline Polymer Builder panel opens
2. Ensure Polyethylene (PE) is the selected Crystal
3. Uncheck Create system for Desmond calculations
4. Click Create New Entry
5. A new entry titled Polyethylene (PE) 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 in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and 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

Figure 6-2. The PE crystal structure.

6. With the PE crystal structure 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, use the Show periodic structure tool window in the bottom right corner to expand the extents and create a P1 Cell
   • For more details on manipulating crystal structures see the Building and Manipulating Crystal Structures tutorial

Figure 6-3. Creating a P1 PE crystal structure.

In this example, the PE crystal structure was expanded to be 12 x 12 x 12 before creating a P1 cell so the system is around 20,000 atoms, similar to the polyethylene semicrystalline systems.

Figure 6-4. Preparing the structure for MD

This system needs to be prepared for MD before we can perform an MD simulation

7. 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 Polyethylene (PE) P1 entry, go to Tasks > Materials > Classical Mechanics > MD Simulations > Prepare for Molecular Dynamics
   • The Prepare for MD panel opens
8. For Job name, enter md_prep_PE_xtal
9. Adjust the job settings () as needed
   • This job requires a CPU host. The job can be completed in just a couple of minutes
10. Click Run
11. Once the job is successfully completed, a new group titled MD: Polyethylene (PE) P1, is now in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
12. Close the Prepare for MD panel

Figure 6-5. Importing the PE polymer structure.

Let’s import an amorphous PE structure

13. Go to File > Import Structures, navigate to the provided tutorial files and Open Section_06 > polymer_builder_PE_amorphous > polymer_builder_PE_amorphous_system-out.cms
    • For more information on building polymers see the Building, Equilibrating and Analyzing Amorphous Polymers tutorial
    • This PE polymer was built with 10 chains and 250 monomers in each chain

Now that we have built a PE crystal structure and imported a PE polymer system we can perform an MD simulation and view the density values as described in Section 4.