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/md_potential_barrier.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 barrier_potential_tutorial, click Save
   • The project is now named barrier_potential_tutorial.prj

Figure 2-3. Viewing the imported system components.

8. Go to File > Import Structures
9. Navigate to where you downloaded the tutorial files (presumably your working directory) and choose system_components.maegz from the provided files
10. Click Open
    • A new entry group is added to the entry list containing three entries; a polypropylene slab, water, and acetone.

In the following two sections, we will study how the two different solvents ingress into the polypropylene slab. Feel free to visualize and stylize the imported structures.

Figure 3-1. Selecting water and including the polypropylene slab.

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 water and includethe entry is represented in the Workspace, the circle in the In column is blue polypropylene slab
   • 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 list 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 3-2. Opening the Disordered System Builder.

2. Go to Tasks > Materials > Structure Builders > Disordered System
   • The Disordered System Builder panel opens
   • water should appear as the only component, otherwise, return to step 1 and ensure that water 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 3-3. Setting parameters in the Components tab.

3. Select Amorphous for the Initial state
4. Change the Number of molecules to 2000
5. Check Substrate
6. Click Import
   • polypropylene_slab should appear next to the import button
   • If it does not import, ensure that the polypropylene_slab was includedthe entry is represented in the Workspace, the circle in the In column is blue in step 1 of this section

Figure 3-4. Defining the substrate 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, ensure that c is chosen as the Crystal vector direction
10. Set Buffer between surface and components to 2 Å
    • This will aid the build and will be reconciled in the later MD stages
11. Set Buffer between components and surface mirror image in the periodic box to 10 Å
12. 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 3-5. Setting the PBC.

13. For Periodic Boundary Conditions (PBC), select Use/expand substrate PBC from the drop-down
14. Go to the Disorder tab

Figure 3-6. Setting the disorder options and running the job.

15. Set the Initial density to 0.9
    • We will pack water in at a relatively high density
16. Ensure Density is chosen as the parameter for Keep constant
17. Change the Job name to disordered_system_polypropylene_water
18. Adjust the job settings () as needed
    • This job requires a CPU host. The job can be completed in 5 minutes on a CPU host
19. If you would like to run the job yourself, click Run. Otherwise, go to File > Import Structures, navigate to the provided tutorial files and Open Section_03 disordered_system_polypropylene_water > disordered_system_polypropylene_water_system-out.cms
20. Close the Disordered System Builder panel
    • In general, always close the Disordered System Builder panel after use. This panel is interactive with the workspace and leaving it open can cause slowdowns

Figure 3-7. Viewing the output of the water polypropylene system.

21. When the job is finished or imported 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_polypropylene_water_all_components_amorphous in the entry list.
    • The gap between the polypropylene slab and water molecules was defined when the interface parameters were set
    • Feel free to stylize and visualize the output system in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed

Figure 3-8. Running the Disordered System Builder.

Repeat the steps in this section to build a disordered system with acetone packed onto the polypropylene slab. Ensure you make the following changes in your procedure:

• Change the Number of molecules to 480
• Set the Initial density to 0.8
• Change the Job name to disordered_system_polypropylene_acetone
• Adjust the job settings () as needed. This job requires a CPU host. The job can be completed in 10 minutes on a CPU host
• If you would like to run the job yourself, click Run. Otherwise, go to File > Import Structures, navigate to the provided tutorial files and Open Section_03 disordered_system_polypropylene_acetone > disordered_system_polypropylene_acetone_system-out.cms

Figure 3-9. Viewing the output of the acetone polypropylene system. .

22. When the job is finished or imported 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_polypropylene_acetone_all_components_amorphous in the entry list.
    • Feel free to stylize and visualize the output system in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed

Figure 4-1. Opening the Set Barrier Potential for MD panel.

1. Ensure that disordered_system_polypropylene_water_all_components_amorphous 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 and includedthe entry is represented in the Workspace, the circle in the In column is blue 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 > Setup Barrier Potential for MD
   • The Set Barrier Potential for MD panel opens

Figure 4-2. Viewing the plane.

3. Click Add Barrier
   • An orange plane is shown where the barrier will be applied
4. Set the Offset to 5.0
   • If you get an error message saying Atom xxx is too close to the barrier, then try decreasing the Offset to 4.0. This is the initial space between the barrier and the atoms or particles.

Figure 4-3. Saving the new Desmond model.

5. Click Apply
   • The Save Desmond Model to File dialogue opens
6. For File name, enter polypropylene_water.cms
7. Click Save
   • A file, polypropylene_water.cms, will be saved to the working directory, and an entry will be imported into the entry list

Figure 4-4. Viewing the output of the Set Barrier Potential for MD panel.

8. Once the new Desmond model is saved and imported, 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 disordered_system_polypropylene_water_all_components_amorphous entry
   • The output looks exactly the same as the output of the disordered system build but now has the impermeable barrier potential set
   • Feel free to stylize and visualize the output system in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed

Figure 4-5. Setting a barrier potential for the polypropylene + acetone system.

Repeat the above steps for disordered_system_polypropylene_acetone_all_components_amorphous and name the new Desmond model polypropylene_acetone.cms. Note that the Offset may need to be decreased to 4.0.

Figure 4-6. Opening the MD Multistage Workflow panel.

Now, let’s run MD simulations to study how water and acetone ingress into polypropylene. The impermeable barrier set atop the cell will restrict all molecules from passing through the ab-plane.

This approach will allow us to reduce simulation time needed to observe substantial ingression, as water and acetone will only be allowed to interact with the polypropylene slab on one side.

9. 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 newly generated Desmond models
10. Go to Tasks > Materials > Classical Mechanics > MD Simulations > MD Multistage Workflow
    • The MD Multistage Workflow panel opens

Figure 4-7. Setting the parameters for Stage 1 and 2.

11. Ensure Apply barrier potential is checked when the panel opens
    • The panel should recognize the selected structures as those with set barrier potentials and will apply them to all stages of the MD simulation
    • If the Apply barrier potential option is grayed out, please ensure you are selecting the Desmond models created with barrier information
12. Maintain Stage 1 as is (Brownian Minimization)
13. Click Append Stage
14. Change the new stage (Stage 2) to Molecular Dynamics
15. Set the Simulation time (ns) to 0.2
    • We will run a very short simulation to collapse the artificial vacuum layer between water/acetone and the polypropylene slab
16. Set the Trajectory Recording interval (ps) to 10
    • This will generate 10 frames in the trajectory
17. Change the Ensemble class to NVT
    • We will hold cell volume constant in this simulation
18. Set the Temperature (K) to 10
19. Set the Time step (fs) to 1
20. Click Append Stage

Figure 4-8. Setting the parameters for Stage 3 and running the job.

21. Change the new stage (Stage 3) to Molecular Dynamics
22. Set the Simulation time (ns) to 10
23. Set the Trajectory Recording interval (ps) to 100
    • This will generate 100 frames in the trajectory
24. Change the Ensemble class to NPT
25. Change the Job name to multistage_simulation_all
26. Adjust the job settings () as needed
    • This job requires a GPU host. The job can be completed in about 2 hours on a GPU host
27. If you would like to run the job yourself, click Run. Otherwise, import the pre-generated Section_04 > multistage_simulation_all > multistage_simulation_all_00n > multistage_simulation_all_00n-out.cms files from the provided tutorial files (where n=1, 2) via File > Import Structures
28. Close the MD Multistage Workflow panel

Figure 4-10. Visualizing the output.

When the job finishes, or after importing, feel free to visualize the output structures. In the figure, the water molecules have been changed to CPK representation for ease of visualization.

Figure 5-1. Viewing the imported system.

1. Go to File > Import Structures
2. Navigate to where you downloaded the tutorial files (presumably your working directory) and choose Section_05 > multistage_simulation_quick_0.2ns > multistage_simulation_quick_0.2ns-out.cms from the provided files
3. Click Open
   • A new entry is added containing the POPC membrane, Na ions, Cl ions, water, and the species of interest, ethanol. This system was constructed and quickly equilibrated using techniques similar to those in Section 3 as well as the Building a Polymer-Polymer Interface Model and Calculating Surfactant Tilt and Electrostatic Potential of a Bilayer System tutorials.
   • Feel free to visualize and stylize the imported structure.

We will study how the ethanol molecules interact with one side of the POPC membrane by imposing a semi-impermeable barrier at the bottom of the periodic cell.

Figure 5-2. Opening the Set Barrier Potential for MD panel.

4. 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 disordered_system_step_3_all_components_amorphous entry
5. Go to Tasks > Materials > Classical Mechanics > MD Simulations > Setup Barrier Potential for MD
   • The Set Barrier Potential for MD panel opens

Figure 5-3. Setting the parameters for the semi-permeable barrier.

6. Click Add Barrier
7. Select the radio-button for the Semi-permeable barrier
8. To define the Non-permeable atoms ASL click the plus sign and click Select
   • The Atom Selection Dialogue opens

Figure 5-4. Selecting the ethanol atoms.

9. Click Clear
   • We will remove all of the atoms currently selected
10. Go to the Molecule tab
11. Select M4
    • M4 corresponds to the 20 ethanol molecules in the system (we can use the Status Bar to confirm molecule types)
12. Click Add
13. Click OK
    • A repulsive potential will be applied exclusively to the 20 ethanol molecules, not allowing them to pass the barrier

Figure 5-5. Visualizing the plane.

14. Change the Relative position of the barrier potential to Below

Figure 5-6. Saving the new Desmond model. 

15. Click Apply
    • The Save Desmond Model to File dialogue opens
16. For File name, enter POPC_ethanol_semi-permeable.cms
17. Click Save

Figure 5-7. Viewing the output of the Set Barrier Potential for MD panel.

18. Once the new Desmond model is saved and imported, 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 disordered_system_step_3_all_components_amorphous entry
    • The output looks exactly the same as the output of the disordered system build but has the semi-permeable barrier potential set
    • Feel free to stylize and visualize the output system in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed

Figure 5-8. Opening the MD Multistage Workflow panel.

Now, let’s run an MD simulation to study if ethanol permeates into the POPC membrane:

19. 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 newly generated Desmond models
20. Go to Tasks > Materials > Classical Mechanics > MD Simulations > MD Multistage Workflow
    • The MD Multistage Workflow panel opens

Figure 5-9. Setting the MD Multistage parameters.

21. Ensure Apply barrier potential is checked when the panel opens
    • The panel should recognize the selected structure as one with set barrier potentials
    • If the Apply barrier potential option is grayed out, please ensure you are selecting the Desmond models created with barrier information
22. Check Remove center of mass motion
    • This option removes the center of mass velocity for the system for all stages of the calculation
23. Change the existing stage (Stage 1) to Molecular Dynamics
24. Set the Simulation time (ns) to 10
25. Set the Trajectory Recording interval (ps) to 10
    • This will generate 1000 frames in the trajectory
26. Change the Ensemble class to NPT

Figure 5-10. Running the MD simulation.

27. Change the Job name to multistage_simulation_POPC_ethanol_wall
28. Adjust the job settings () as needed
    • This job requires a GPU host. The job can be completed in about 1 hour on a GPU host
29. If you would like to run the job yourself, click Run. Otherwise, import the pre-generated Section_05 > multistage_simulation_POPC_ethanol_wall > multistage_simulation_POPC_ethanol_wall-out.cms files from the provided tutorial files via File > Import Structures
30. Close the MD Multistage Workflow panel

Figure 5-11. Visualizing the output.

When the job finishes, or after importing, feel free to visualize the output structure. In the figure, the water molecules have been hidden and the ethanol molecules have been changed to CPK representation for ease of visualization.