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/cluster_analysis.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 clusters_tutorial, click Save
   • The project is now named clusters_tutorial.prj

Figure 2-3. The entry list after importing.

Our system will contain three components, Rha-C10-C10, decane and water. Before building them into a disordered system, we need to prepare one entry for each component.

8. Go to File > Import Structures
9. Navigate to where you downloaded the tutorial files, choose input_molecules.mae and click Open
   • Three entries are added to the entry list: Rha-C10-C10, decane and water
   • Rha-C10-C10 is includedthe entry is represented in the Workspace, the circle in the In column is blue
   • Feel free to visualize or stylize any of these molecules

Note: If you would prefer to prepare these input structures yourself, feel free to practice doing so using the 2D Sketcher or by importing from PubChem or other depositories. For a reminder on using the 2D Sketcher, see Introduction to Materials Science Maestro. Always be mindful of stereochemistry when performing 2D to 3D conversion, particularly when importing downloaded structures.

Note: If you will be using these structures (or any structures) in future projects commonly, you can avoid redrawing them by saving them to the Import Favorite Structures panel

Figure 3-1. Selecting the entries.

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 workspace
   • 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 the rows in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion

Figure 3-2. The Disordered System Builder panel.

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

Figure 3-3. Setting the Components.

The Disordered System Builder panel facilitates building a randomized multi-component mixture of a given composition, either on its own, or on a substrate. In this case, we will pack the three components with no substrate.

Note that in addition to the Disordered System Builder, the Solvation Builder panel can be useful in constructing very large, solvated systems.

We will construct a box of 100 Rha-C10-C10 molecules, 50 decane molecules and 26500 water molecules which is ~5% surfactant by weight.

3. Change Number of molecules to 26650
4. Change the Molecules for Rha-C10-C10 to 50, decane to 100 and water to 26500
5. For Periodic Boundary Conditions, choose Create New Cubic PBC from the dropdown menu
   • The resultant box will be cubic (a = b = c, all angles = 90º)
6. For Initial state, choose Tangled chain
   • Visit the documentation for the differences between the choices. In this case, tangled chain should allow for the quickest build

Note: The Disordered Options button allows access to other useful settings, including setting a target build density. In this case, the defaults are sufficient for constructing our initial box in preparation for MD

7. Change the Job name to disordered_system_rha_decane
8. Adjust the job settings () as needed
   • This job requires a CPU host. The job can be completed in about 30 minutes
9. If you would prefer not to run the job, import Section_03 > disorederd_system_rha_decane > disordered_system_Rha_decane_system-out.cms from the provided tutorial files. Otherwise, click Run
10. Close the Disordered System Builder

Figure 3-4. Output of the build.

When the job finishes or after importing, a new entry appears titled disordered_system_rha_decane_all_components_amorphous

11. 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 this new entry, and feel free to visualize the output
    • Recall that this has not yet been equilibrated by molecular dynamics (MD), and is just a starting model to now submit for an MD simulation
    • Notice that the molecules are randomly placed. Until the MD stage, no assembly should be expected

Figure 3-5. Using the WAM Button.

12. Use the WAM () button to access the MD Multistage Workflow panel
    • Alternatively, go to Tasks > Materials > Classical Mechanics > MD Simulations > MD Multistage Workflow

Figure 3-6. Setting up and running the MD Multistage workflow.

We will now proceed to run a relaxation procedure followed by a relatively short ‘production’ level MD simulation. In this instance, we know in advance that the system assembles within ~30 nanoseconds. So, we will run a 30 ns simulation to be used for the Cluster Analysis.

In practice, you may wish to first run a shorter simulation (~1-5 ns) before committing to a more computationally intensive run, and then follow this short simulation with a substantially longer ‘production’ level run (100+ ns)

13. Ensure that Project Table (1 selected entry) is chosen for Use structures from
14. Check Relaxation protocol and ensure that it is set to Materials relaxation
    • This protocol consists of three stages which are sufficient for densifying simple systems like this one: 20 ps NVT Brownian minimization at 10K, 20 ps NPT Brownian minimization at 100K, 100 ps NPT MD stage at 300K
15. For the fourth stage, ensure that the Stage type is set to Molecular Dynamics
16. Change the Simulation time to 30 ns and the Recording interval to 100 ps
    • Note that the Recording interval is an important choice, because it will have the biggest impact on the trajectory file size. In this case, the output will be ~500 MB
17. Change the Job name to multistage_simulation_rha_decane
18. Adjust the job settings () as needed
    • This job requires a GPU host. The job can be completed in about 5 hours on a single GPU
19. If you would prefer not to run the job, import Section_03 > multistage_simulation_rha_decane > multistage_simulation_rha_decane-out.cms from the provided tutorial files. Otherwise, click Run
20. Close the MD Multistage Workflow panel

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.

Figure 3-7. Output of the MD simulation.

When the job finishes or after importing, a new entry appears also titled disordered_system_rha_decane_all_components_amorphous

21. 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 this new entry, and feel free to visualize the output

 

Note: It is important to remember that the system is periodic, meaning that the unit cell is infinitely repeated by translation along its a, b, and c vectors. When visualizing the clusters in this tutorial, be aware that an aggregate at the edge of the box or outside of the box may be in contact with other groups. For a detailed discussion of periodic boundary conditions, see the Building and Manipulating Crystal Structures tutorial.

 

Note: While the aggregate being near the boundary is only a visual matter, there are tools for changing the position of the periodic boundary conditions (PBCs) if you prefer. For example, right-click on an atom in the workspace and click Center Cell on Atom or use the Manipulate Cell tool to adjust the PBCs

Figure 3-8. Renaming the entry.

22. Rename the entry by double-clicking on disordered_system_rha_decane_all_components_amorphous in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and typing surf_cluster

Figure 3-9. Adjusting the playback settings and viewing the trajectory.

Ensure that the trajectory loads:

23. Double-click on the button in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
    • If a Missing Trajectory error appears, click Import Trajectory and select the multistage_simulation_rha_decane_5_trj directory in the cluster_analysis folder

The trajectory should now be loaded, as indicated by the presence of the Trajectory Player at the bottom of the workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

24. Click on the Playback Settings button
25. Set smoothing to 3 and turn off looping
26. Close the Playback Settings pop-up and click on the Play button on the left side of the Trajectory Player menu to view the trajectory
27. Once you have viewed the trajectory, close the Trajectory Player with the in the Trajectory Player menu

Figure 3-10. Selecting the solvent molecules.

For ease of visualization, we are going to hide the solvent water molecules. 

28. From the main menu, go to Select > Solvent

Figure 3-11. The selected solvent molecules.

All of the water molecules are selected in the workspace.

Figure 3-12. Hiding the water molecules.

29. Go to the Style menu and choose Undisplay Selected Atoms
    • The water molecules are hidden in the workspace
30. Click outside of the unit cell to deselect the water molecules

Figure 3-13. The workspace after hiding solvent.

Only the Rha-C10-C10 and decane are shown.

Figure 3-14. Changing to CPK representation.

31. Go to the Style menu and choose Apply CPK Representation

 

 

Figure 3-15. The workspace after changing the representation.

The style for the Rha-C10-C10 and decane molecules is updated to CPK representation.

 

Note: The CPK percentage can be adjusted in the Preferences menu. Go to Molecular Representation > Atoms and Bonds or search “CPK” or “Atoms and Bonds” to find the CPK percentage slider. For this tutorial, the percentage used is 50, but this can be adjusted to your preference. 

Figure 4-1. Loading the trajectory and setting the interval.

1. With surf_cluster 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 and included in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed, go to Tasks > Materials > Classical Mechanics > Trajectory Analysis > Cluster Analysis Calculations
   • The Cluster Analysis panel opens
2. Click Load from Workspace
   • Be patient, loading can take a few seconds depending on the size of the trajectory
   • surf_cluster appears next to the load button
3. Click Trajectory Frames...
   • The Trajectory Frames filter opens
4. Set the range to 0 - 4 ns (0 - 40 frames) and click OK
   • The Step size option can be used if you wish to use every n-th frame rather than all of the frames over a range

Figure 4-2. Defining the cluster constituents.

5. Keep the Maximum neighbor distance at 3.00 Å
   • This is the radius for defining a neighbor in the cluster-defining algorithm. 3.00 Å is recommended for atomistic systems, and 6.00-9.00 Å for coarse-grained systems

Use the Cluster constituents section of the panel to decide which components can qualify as part of a cluster.

6. From the Molecular species dropdown, deselect H2O
   • This ensures that the water molecules are excluded from the cluster analysis calculation
   • Alternatively, use the a Molecular weight range to discriminate components

Figure 4-3. Naming and running the job.

7. Keep the remaining defaults and set the Job name to cluster_analysis_short
8. Adjust Job settings () as needed, and click Run
   • The job takes ~10 minutes on a CPU host

Note: Use the Extract clusters at last frame option if you want to create and return an entry for each of the clusters in the last frame for visualization or subsequent calculation. We will do so in Section 5.

Note: Use the Calculate density profile with resolution option if you want to generate high resolution radial density profiles, measuring the spatial distribution of species relative to the cluster center of mass.

Figure 4-4. Visualizing the Cluster Analysis output in the workspace (after renaming and changing to CPK representation).

9. Close the Cluster Analysis Calculations panel
10. Once the job is incorporated, 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 new output file: disordered_system_rha_decane_all_components_amorphous
    • The output in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed is the last frame in the trajectory range
    • The clusters are automatically colored (note again that some clusters are contiguous across the periodic boundary conditions and that the boundaries are purely visual)
11. Let’s rename again. Double-click disordered_system_rha_decane_all_components_amorphous in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and change to surf_cluster_short

Feel free to repeat any stylizing steps from Section 3 above, including switch the style to CPK Representation

Figure 4-5. The Cluster Analysis Viewer panel.

12. To analyze the results panel for the calculation, use the Workflow Action Menu (WAM) button () or go to Tasks > Materials > Classical Mechanics > Trajectory Analysis > Cluster Analysis Results
    • The Cluster Analysis Viewer panel opens
    • If the graphs are not populated by default, use the Load from Workspace button

 

The top graph shows the number of clusters over time. We can choose to display the average cluster size over time as well.

The bottom graph shows the number of molecules in a given cluster over time. The default lines are the first and second largest clusters, but additional clusters can be displayed. In Section 5, we will explore this graph in much more detail.

Figure 4-6. The Cluster Compositions tab.

13. Change to the Final Clusters tab

At the final frame in the trajectory range specified, there are 6 clusters present (displayed in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed in the various coloring schemes). You can select a cluster in the workspace by clicking and highlighting the corresponding row in the table shown in the Figure. 

This data indicates how many Rha-C10-C10 and decane molecules comprise each cluster in the final frame as well as the Average R_g (radius of gyration) and Average Eccentricity

14. Close the Cluster Analysis Viewer

Figure 5-1. Setting the Cluster Analysis parameters for the full trajectory.

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 and includethe entry is represented in the Workspace, the circle in the In column is blue the original surf_cluster entry, and return to Tasks > Materials > Classical Mechanics > Trajectory Analysis > Cluster Analysis Calculations
   • The Cluster Analysis panel opens
2. Repeat Steps 2-6 from Section 4 with the exception of now including the entire trajectory range: 0 - 30.00 ns (0 - 301 frames)
   • This job will repeat the analysis of the previous, but now with the remainder of the trajectory
3. Check Extract clusters at last frame
   • The output will include both the cluster analysis output entry as well as a standalone entry of the extracted cluster (or several entries in cases with several clusters)

Note: Use the Calculate density profile with resolution option if you want to generate high resolution radial density profiles, measuring the spatial distribution of species relative to the cluster center of mass.

4. Set the Job name: cluster_analysis_full
   • The panel should match that which is shown in the Figure

This job takes ~45 minutes on a CPU host. If you’d like to skip running the job and use a pre-generated output, proceed to Step 5 below. If you’d like to run the job, adjust Job settings () as needed, click Run, then skip to Step 8.

Figure 5-2. Importing pre-generated results.

5. Go to File > Import Structures
   • The import menu opens
6. In the downloaded tutorial files, select the Section_05 > cluster_analysis_full > cluster_analysis_full_out.maegz file in the cluster_analysis_full directory
7. Click Open
   • A group titled cluster_analysis_full_out (1) containing MD: system_builder_rha_decane (1) appears in the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
   • The group contains one entry: disordered_system_rha_decane_all_components_amorphous

Figure 5-3. Visualizing the Cluster Analysis output in the workspace (after renaming and changing to CPK representation).

8. Once the job is complete, or if you have imported the pregenerated results file, 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 new output file: disordered_system_rha_decane_all_components_amorphous
   • This is the last frame in the trajectory range
   • The clusters are automatically colored. In this case, the final frame is only one cluster
   • The other entry, cluster 1, is the extracted clusters
9. Let’s rename again. Double-click disordered_system_rha_decane_all_components_amorphous in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and change to surf_cluster_full

 

Feel free to repeat any stylizing steps from Section 3 above, including switch the style to CPK Representation

Figure 5-4. The number of molecules over time for the four largest clusters.

10. To analyze the results panel for the calculation, use the Workflow Action Menu (WAM) button () or go to Tasks > Materials > Classical Mechanics > Trajectory Analysis > Cluster Analysis Results
    • The Cluster Analysis Viewer panel opens

The top graph again shows the number of clusters over time.

The bottom graph can be adjusted to present additional data:

11. Increase the counter to 4 for Plot for largest cluster(s)
    • Data for the first four largest clusters over time appears in the graph window. Hover the mouse over the graph to view corresponding (x, y) coordinates
    • Notice that after about 12 ns, all of the molecules have formed two clusters

Figure 5-5. The mass-weighted radius of gyration over time for the four largest clusters.

12. Keep the counter on 4 for Plot for largest cluster(s), and change the Property to Mass-weighted radius of gyration
    • Data for the mass-weighted radius of gyration versus time for the four largest clusters appears in the graph window

Note: Changing the Calculate radius of gyration using the radio button in the initial calculation panel allows you to compute R_g via two different methods. See the documentation for further details.

Figure 5-6. The fractional anisotropy over time for the four largest clusters.

13. Keep the counter on 4 for Plot for largest cluster(s), and change the Property to Fractional Anisotropy
    • Data for the fractional anisotropy versus time for the four largest clusters appears in the graph window
    • The relative anisotropy is a measure of how spherical versus linear a cluster is: an anisotropy of 0 representing a perfect sphere, and an anisotropy of 1 representing a line

 

Feel free to explore the other available properties. You can also navigate to the Final Clusters tab, though in this case, as expected, all of the molecules are part of the two clusters present in the final frame. Details about the various properties are available in the documentation.

Finally, note that two other entries are available in the entry list containing the extracted clusters if helpful for further analysis.