1. Double-click the Materials Science icon on your desktop
   • (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/api_miscibility.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 api_miscibility_tutorial, click Save
   • The project is now named api_miscibility_tutorial.prj

Figure 2-3. Importing one input file.

In the next section, we will study four organic molecules. These starting structures have been provided:

8. Go to File > Import Structures
9. Navigate to where you downloaded the provided tutorial files, choose input_molecules.mae and click Open
   • A new entry group containing four entries is added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion

Note: The structure for PVP is not provided. We will learn to build it with the Polymer Builder in Section 3.

Figure 2-4. The entry list after importing.

Optional: If you would prefer to practice preparing the components yourself, draw the molecules in the 2D Sketcher or import from the PDB or other sources. For background on using the sketcher, see the Introduction to Maestro for Materials Science tutorial.

Figure 3-1. Ibuprofen, selected in the entry list and included in the workspace.

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

For amorphous ibuprofen, we will study the S isomer, which is the more biologically active enantiomer. If you wish, you can confirm that the provided input is the S isomer by visually inspecting or using Style > Apply Labels > Chirality.

Figure 3-2. Setting the Potential tab in the Conformational Search panel.

For our MD simulation, we will construct a cell containing many of these ibuprofen molecules. Though the molecule will relax during the equilibration, in cases with somewhat flexible molecules, it is a good practice to first perform a conformational search on the input molecule such that the conformation in the initial cell is relatively low energy.

2. Go to Tasks > Browse All > MacroModel > Conformational Search
   • The Conformational Search panel opens
3. For Solvent, choose none from the option-menu
4. Go to the CSearch tab

Figure 3-3. Setting the CSearch tab and running the Conformational Search panel.

For more information about the options chosen here, visit the thorough help documentation or the Conformation Analysis for Small Molecules tutorial. In general, the defaults are sufficient for a basic conformational search.

5. For Method, select Low-mode sampling and uncheck Multi-ligand
6. Ensure Perform automatic setup during calculation is checked
7. Change the Maximum number of steps to 200
8. Change the Job name to mmod_csearch_ibuprofen
9. Adjust the job settings () as needed. This job requires a CPU host and takes less than a minute. Click Run
10. Close the Conformational Search panel
11. Once the job is successfully completed, a new mmod_csearch_ibuprofen-out1 group 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
    • The number of conformers output may vary depending on your software version or any of your previous settings in the Conformational Search panel.

Note: The option to uncheck Retain mirror-image conformations is available, though it is recommended to keep it checked when stereochemistry is a critical factor. For this particular example, the setting is not critical.

Figure 3-4. Viewing the relative energies of the conformers.

The output from the conformational search ranks the structures from top to bottom from lowest energy to highest energy (dictated by the force field). We can view the relative energies (in kJ/mol) directly in the entry list:

12. Use the table settings icon   at the top of the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion to add the Relative Potential Energy-S-OPLS property (Show Property > Choose > Relative Potential Energy-S-OPLS)
    • The relative energies of the conformers are visible directly in the entry list

Figure 3-5. Opening the Disordered System Builder panel.

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 and includethe entry is represented in the Workspace, the circle in the In column is blue the first ibuprofen entry in the mmod_csearch_ibuprofen-out1 group
14. Go to Tasks > Materials > Structure Builders > Disordered System
    • The Disordered System Builder panel opens

Figure 3-6. Setting up the Components tab and running the job. 

We will construct a cell containing 512 ibuprofen molecules (16896 atoms).

15. For Initial state, choose Amorphous
    • Visit the documentation for the differences between the choices.
16. For Number of molecules, input 512
    • The number of ibuprofen molecules updates in real-time
17. Change the Job name to disordered_system_ibuprofen
18. Adjust the job settings () as needed
    • This job requires a CPU host. The job can be completed in about 5 minutes on a CPU host
19. If you would like to run the job yourself, click Run. Otherwise, import the pregenerated disordered_system_ibuprofen_system-out.cms file from the provided tutorial files via File > Import Structures in the Section_03 > disordered_system_ibuprofen directory
20. Close the Disordered System Builder

Note: For additional practice using the Disordered System Builder and more detail on the various parameters, see the Disordered System Building and MD Multistage Workflows tutorial.

Note: In general, always close the Disordered System Builder after use. This panel is interactive with the workspace and leaving it open can cause slowdowns

Note: The default initial density of 0.5 g/cm³ will generate a very low density cell. However, the subsequent molecular dynamics protocols will serve to compress the structure. Alternative approaches are certainly reasonable, including trying to build an initial cell closer to the experimental density.

Figure 3-7. The cell after the disordered system build.

When the job is finished or after importing, a new entry titled disordered_system_ibuprofen_all_components_amorphous is available in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion. We will return to it later.

Figure 3-8. The lowest energy structure of sorbitol as determined by the conformational search.

Water and cyclohexane have fewer degrees of conformational freedom, so it is not necessary to perform conformational search. Sorbitol, however, is a very flexible molecule, and so we may want to perform a conformational search on it:

21. Repeat Steps 1-12 for the provided sorbitol entry to obtain a low energy conformation. Name your job mmod_csearch_sorbitol

Figure 3-9. Three solvent systems in the workspace. The cells are tiled to allow visualization of all three, but this is not necessary to do.

Now, let’s proceed to construct cells for water, cyclohexane and sorbitol.

22. Individually Repeat Steps 13-21 for the provided water and cyclohexane entries, as well as the lowest energy conformer from the sorbitol conformational search. For the quantity of molecules in each box, use the following:
    • Water: 8000 molecules
    • Cyclohexane: 1000 molecules
    • Sorbitol: 729 moleculesName the jobs disordered_system_water, disordered_system_cyclohexane and disordered_system_sorbitol. Otherwise, maintain all of the same settings. Note that all of these structures are also available for importing from the provided tutorial files: disordered_system_*component*_system-out.cms (component = water cyclohexane, sorbitol) in the Section_03 directory  

Note: The default water model in the Disordered System Builder is SPC. This can be adjusted in the Disorder Options on the Disorder tab.

Figure 3-10. The Groups tab.

We will return to all four amorphous cells shortly. Before we do so, let us now construct the PVP system.

23. Go to Tasks > Materials > Structure Builders > Polymer
    • The Polymer Builder panel opens
    • For a detailed overview of using the polymer builder, visit the Building, Equilibrating and Analyzing Amorphous Polymers tutorial
24. In the End groups section of the panel, maintain the defaults to terminate the chains with H and not include any cascader
25. In the Monomers section of the panel, choose n-vinyl_pyrrolidone

Figure 3-11. The Composition tab.

26. Go to the Composition tab
27. Change the Number of monomers to 20
    • Each chain will contain 20 PVP monomers

Figure 3-12. The Amorphous Cell tab.

28. Go to the Amorphous Cell tab
29. Check Create amorphous cell
30. Choose Boltzmann at 300.00 K for the Dihedral angle distribution
31. Change the Number of polymers to 60
    • The cell will contain 60, 20-mers which is 20520 atoms
32. Change the Job name to polymer_builder_PVP
33. Adjust the job settings () as needed
    • This job requires a CPU host. The job can be completed in about 30 minutes on a CPU host
34. If you would like to run the job yourself, click Run. Otherwise, import the pregenerated polymer_builder_PVP_system-out.cms file from the provided tutorial files via File > Import Structures in the Section_03 > polymer_builder_PVP directory
35. Close the Polymer Builder

Note: If you were interested in creating a disordered system containing the polymer as one of several components, rather than using the Create amorphous cell option, you should run the job with Create amorphous cell unchecked to generate a single polymer chain and then use this output entry as a component in a new disordered system build.

Figure 3-13. The amorphous polymer cell output from the polymer builder.

When the job is finished or after importing, a new entry titled amorphous poly(N-vinyl pyrrolidone) is available in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.

You should now have prepared five amorphous cells: ibuprofen, water, cyclohexane, sorbitol and PVP. We will prepare two crystalline cells in Section 4, and then return to these cells in Section 5 to perform MD simulations.

Figure 4-1. Selecting, including and stylizing the crystal structure.

1. Go to File > Import Structures
2. Navigate to where you downloaded the provided tutorial files, choose Section_04 > ibuprofen_IBPRAC_P21-c.cif and click Open
   • 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
3. 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 IBPRAC entry from the entry list
4. Use the Style palette  () to change the rendering to ball-and-stick representation () and Color Atoms by Element

Figure 4-2. Building the unit cell.

The asymmetric unit contains one ibuprofen molecule. It is first useful to visualize the full unit cell and to recalculate the bond orders. This is important to ensure correct force-field-typing in later steps.

5. Click on the button to open the Periodic Structure Tool Window
6. Go to Build Cell
7. Choose Translate to First Unit Cell and choose Intact Molecules
8. Choose Recalculate Bond Orders
9. Click Apply

Note: If you are new to working with periodic systems in Materials Science Maestro, visit the Building and Manipulating Crystal Structures tutorial.

Figure 4-3. Expanding the extents (the figure shows the structure after clicking Apply).

For the MD simulation, we want a box similar in size to those prepared in Section 3. To do so for this periodic structure:

10. Click on the button to open the Periodic Structure Tool Window
11. Go to Build Cell, click Extents and for +A, +B and +C, input 4, 4 and 4
12. Click Apply
    • The workspace is updated to show an expanded cell, now with 500 molecules, similar in size to the amorphous cell
    • Next to the Periodic Structure Tool icon, the green text indicates CELL: 5 x 5 x 5

Figure 4-4. Changing the expanded cell into a new P1 cell.

13. Click on the button again to open the Periodic Structure Tool Window
14. Choose Make P1 Cell
    • A new entry is added to the bottom of the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion titled IBPRAC P1
    • It is includedthe entry is represented in the Workspace, the circle in the In column is blue in the workspace by default

Figure 4-5. The new P1 cell for the second polymorph.

The steps for the second polymorph have been performed for you:

15. Go to File > Import Structures
16. Navigate to where you downloaded the provided tutorial files, choose Section_04 > 2001546_P1_system.mae and click Open
    • 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 titled 2001546 P1

You now have two prepared crystalline cells of the ibuprofen polymorphs. 

Figure 4-6. Selecting the structures and running Prepare for MD.

In order to run an MD simulation on these periodic structures, one final step must be performed. Specifically, we must use the Prepare for MD panel to clean up bond orders, select a force field and create a simulation box that is ready for the MD simulation with Desmond, our MD engine.

17. 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 IBPRAC P1 and 2001546 P1 entries from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
18. Go to Tasks > Materials > Classical Mechanics > MD Simulations > Prepare for Molecular Dynamics
    • The Prepare for MD panel opens
19. Ensure that Use structures from shows Project Table (2 selected entries) and retain the other defaults
20. Change the Job name to md_prep_crystals
21. Adjust the job settings () as needed
    • The job can be completed in about 1 minute on a CPU host
22. Click Run
23. Close the Prepare for MD panel

Note: This step is not necessary for the amorphous systems because the Disordered System Builder panel includes this setup by default.

Figure 4-7. Crystalline outputs ready for MD.

The output will be two new entries named IBPRAC P1 and 2001546 P1 again, but now in entry groups titled MD: IBPRAC_P1_system (1) and MD: 2001546_P1_system (1), respectively. The structures will look exactly the same, but now they also contain the necessary setup data to perform an MD simulation.

Figure 5-1. Selecting the entries and 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 the five amorphous cells (ibuprofen, water, cyclohexane, sorbitol and PVP) 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 > MD Simulations > MD Multistage Workflow
   • The MD Multistage Workflow panel opens

Figure 5-2. Setting up the MD Multistage Workflow.

3. Ensure that Use structures from shows Project Table (5 selected entries)
   • Otherwise, return to Step 1 above
4. Check Relaxation protocol and choose Compressive
5. Change the next stage (Stage 8) to Molecular Dynamics
6. Set the Simulation time (ns) to 20
7. Set the Trajectory Recording interval (ps) to 200
   • This will generate 100 frames in the trajectory
8. Click Append Stage
   • A 9th stage appears in the workflow
9. Change the new stage (Stage 9) to Analysis
10. Change the Job name to multistage_simulation_amorphous_all
11. Adjust the job settings () as needed
    • This job requires a GPU host. Each job can be completed in about 4 hours on a GPU host
12. If you would like to run the job yourself, click Run. Otherwise, import the pre-generated multistage_simulation_amorphous_all_00n-out.cms (where n = 1-5) files from the provided tutorial files via File > Import Structures in the Section_05 > multistage_simulation_amorphous_all directory
    • 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
13. If running the job, wait for all five jobs to submit, then close the MD Multistage Workflow panel

Figure 5-3. Output from the MD simulations on the amorphous cells. Just the cyclohexane cell is shown.

After the job completes or after importing, five new entries are added to the entry list.

Feel free to visualize the cells and the trajectories if you are interested. In Section 6 we will study the bulk properties.

If you are unfamiliar with visualizing trajectories, visit the Building, Equilibrating and Analyzing Amorphous Polymers tutorial.

Figure 5-4. Selecting the entries, opening and resetting the MD Multistage Workflow panel.

14. 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 crystalline cells from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
    • Be sure to select the two outputs from the Prepare for MD panel
15. Go to Tasks > Materials > Classical Mechanics > MD Simulations > MD Multistage Workflow
    • The MD Multistage Workflow panel opens
16. Use the reset button () to reset the panel settings

Figure 5-5. Setting up the MD Multistage Workflow.

17. Ensure that Use structures from shows Project Table (2 selected entries)
    • Otherwise, return to Step 14 above
18. Change the stage (Stage 1) to Molecular Dynamics
19. Set the Simulation time (ns) to 20
20. Set the Trajectory Recording interval (ps) to 200
21. Click Advanced Options

Figure 5-6. Advanced Options.

22. Change the Coupling Style to Flexible-angle and click OK
    • This will allow for the shape of the crystal structure cell (angles and lengths) to relax. This option should not be used with liquid systems.

Figure 5-7. Analysis stage, naming and running the job.

23. Click Append Stage
    • A 2nd stage appears in the workflow
24. Change the new stage (Stage 2) to Analysis
25. Change the Job name to multistage_simulation_crystals
26. Adjust the job settings () as needed
    • This job requires a GPU host. The job can be completed in about 3 hours
27. If you would like to run the job yourself, click Run. Otherwise, import the pre-generated multistage_simulation_cystals_00n-out.cms (n = 1, 2) files from the provided tutorial files via File > Import Structures in the Section_05 > multistage_simulation_crystals directory
28. If running the job, wait for both jobs to submit, then close the MD Multistage Workflow panel

Figure 5-8. Output from the MD simulations on the crystalline cells. Just the IBPRAC cell is shown.

After the job completes or after importing, two new entries are added to the entry list.

Feel free to visualize the cells and the trajectories if you are interested. In Section 6 we will study the bulk properties.

Figure 6-1. Selecting the amorphous ibuprofen output and opening the MS MD Trajectory 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 and includethe entry is represented in the Workspace, the circle in the In column is blue the amorphous ibuprofen cell output from the MD simulation
2. Go to Tasks > Materials > Classical Mechanics > Trajectory Analysis > MS MD Trajectory Analysis
   • The MS MD Trajectory Analysis panel opens
3. Click Load from Workspace
   • The Simulation Details tab is populated with information about the loaded trajectory

Note: The analysis will be provided for whichever stage in the MD Multistage Workflow directly preceded the analysis stage. In this case, that is the 20 ns MD.

Figure 6-2. Bulk Properties tab.

4. Go to the Bulk Properties tab

This tab provides data for the trajectory, including Specific Heat Capacity (top of the panel), Volume and Density (top graph) and Cohesive Energy, Heat of Vaporization and Solubility Parameters (bottom graph).

The data can be analyzed over the entire trajectory or for some portion. The Set Range button can be used to define a range, or the Final 20% button can be used to plot data only from the last 20% of the trajectory.

The histogram associated with each graph shows the distribution, which is useful for determining if the cell is equilibrated.

Figure 6-3. Density and cohesive energy for amorphous ibuprofen.

Here, we are interested in three properties: density, cohesive energy and solubility parameters.

5. Use the dropdown for the top graph to change to Density
   • Visual inspection of the density over time as well as of the histogram indicates that this cell is fairly well equilibrated
   • The Average and Standard Deviation is printed above the graph

The bottom graph shows the Cohesive Energy.

Figure 6-4. Density and cohesive energy for the last 20% of the trajectory.

6. Click Final 20%
   • We will record the density and cohesive energy from the last 20% of the trajectory
   • The Average and Standard Deviation is printed above the graph

Figure 6-5. Solubility parameter for the last 20% of the trajectory.

7. Change the bottom graph dropdown to Solubility parameter
   • To view the parameter for the entire trajectory, use the Set Range button. In this case, again we will record the parameter from the last 20%
   • The Average and Standard Deviation is printed above the graph

The provided parameter is the Hildebrand solubility parameter, which is the square root of the cohesive energy density. The parameter estimates miscibility based on the qualitative concept of ‘like dissolves like.’ In particular, materials with similar Hildebrand solubility parameters are likely to be miscible. 

Note that this parameter is different from the Hansen solubility parameter. The Hansen solubility parameter separates contributions from the vdW and electrostatic energies and are also available in the dropdown.

See Solubility parameters: DOI:10.1021/cr60298a003

Also note that this parameter is different from intrinsic solubility (S or logS).

Figure 7-1. Selecting the entries and opening the Disordered System Builder.

1. Returning to the top of your entry list, 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 water and ibuprofen
   • Be sure for ibuprofen to select the low energy conformer from the conformation search
2. Go to Tasks > Materials > Structure Builders > Disordered System
   • The Disordered System Builder panel opens
   • When the panel opens, as in the Figure, water and ibuprofen should be listed in the components table. If your panel does not much the Figure, return to the previous step and check your selections

Figure 7-2. Setting up the Disorder System Builder and running the job.

We wish to prepare a ~20 wt% ibuprofen in water solution:

3. For Initial state, choose Amorphous
4. Change the Number of molecules to 7500
5. Change the Molecules for water in the Components table to 7340
   • The number of ibuprofen molecules should update automatically to 160. The wt % will update as well
6. Change the Job name to disordered_system_ibuprofen_water
7. Adjust the job settings () as needed
   • This job requires a CPU host. The job can be completed in about 20 minutes on a CPU host
8. If you would like to run the job yourself, click Run. Otherwise, import the pregenerated Section_07 > disordered_system_ibuprofen_water > disordered_system_ibuprofen_water_system-out.cms file from the provided tutorial files via File > Import Structures
9. Close the Disordered System Builder

Figure 7-3. The ibuprofen/water cell after the disordered system build.

When the job is finished or after importing, a new entry titled disordered_system_ibuprofen_water_all_components_amorphous is available in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion

Figure 7-4. The ibuprofen/cyclohexane cell after the disordered system build.

10. Repeat Steps 1-10 for ibuprofen and cyclohexane. In this case, construct a cell with 1450 total molecules (1316 cyclohexane, 134 ibuprofen). Name the job disordered_system_ibuprofen_cyclohexane

Figure 7-5. The mixed systems stylized and tiled in the workspace. Note, you do not need to tile the workspace, it is just for visualizing here. 

By default, the mixed component systems will be colored by component. Feel free to stylize the cells however you like. For ease of visualization, we have colored by element and changed the representation of the ibuprofen molecules to CPK and the solvent molecules to wireframe.

Figure 7-6. Selecting the entries, opening and resetting the MD Multistage Workflow panel.

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 the two mixed amorphous cells (ibuprofen/water and ibuprofen/cyclohexane) in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
12. Go to Tasks > Materials > Classical Mechanics > MD Simulations > MD Multistage Workflow
    • The MD Multistage Workflow panel opens
13. Reset the panel using reset button() in the bottom left corner of the panel

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

14. Ensure that Use structures from shows Project Table (2 selected entries)
    • Otherwise, return to Step 12 above
15. Check Relaxation protocol and choose Compressive
16. Change the next stage (Stage 8) to Molecular Dynamics
17. Set the Simulation time (ns) to 20
18. Set the Trajectory Recording interval (ps) to 200
    • This will generate 100 frames in the trajectory
19. Click Append Stage
    • A 9th stage appears in the workflow
20. Change the new stage (Stage 9) to Analysis
21. Change the Job name to multistage_simulation_mixed_systems
22. Adjust the job settings () as needed
    • This job requires a GPU host. Each job can be completed in about 4 hours on a GPU host
23. If you would like to run the job yourself, click Run. Otherwise, import the pre-generated multistage_simulation_mixed_systems_00n-out.cms (where n = 1, 2) files from the provided tutorial files via File > Import Structures in the Section_07 > multistage_simulation_mixed_systems directory
24. If running the job, wait for both jobs to submit, then close the MD Multistage Workflow panel

Figure 7-8. Output from the MD simulations on the mixed cells. Just the ibuprofen/water cell is shown in the figure.

After the job completes or after importing, two new entries are added to the entry list.

Figure 7-9. The outputs tiled in the workspace.

Again, by default, the mixed component systems will be colored by component. Feel free to stylize the cells however you like. For ease of visualization, we have colored by element and changed the representation of the ibuprofen molecules to CPK and the solvent molecules to wireframe.

In the Figure, we show the two outputs tiled. Notice that in the case of the water system, complete phase separation is observed (recall that because of periodic boundary conditions, the cluster of ibuprofen may appear across the cell, but is actually part of the larger cluster). In the case of the cyclohexane system, a more homogeneous mixture is visible.

Figure 7-10. The ibuprofen/water cell after adding +1 Extents in +A, +B and +C.

The phase separation in the ibuprofen / water cell is most clearly visualized by including additional periodic images in the workspace. Optionally use the button to open the Periodic Structure Tool Window and add extents to visualize additional unit cells.

Note: When adding extents in large MD systems, be patient after pressing apply. With so many atoms, it will take a few moments to update.

Figure 7-11. Shifting the center of the cell with respect to the ibuprofen cluster.

25. For better visualization of the ibuprofen cluster, select an atom at the center of the cluster
26. Right click and choose Center cell on Atom
    • The simulation box will be centered around the selected atom and the cluster will appear whole.

Feel free to visualize the cells and the trajectories if you are interested.