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/surfactant_tilt.zip
5. After downloading the zip file, unzip the contents in your Working Directory 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 surfactant_tilt, click Save
   • The project is now named surfactant_tilt.prj

Figure 3-1. Drawing protonated SLES in the 2D Sketcher.

If you are already familiar with preparing these inputs, go to File > Import Structures, navigate to the provided tutorial files and import input_molecules.mae, then skip to Section 4. Otherwise, follow these steps:

1. From the main menu, go to Edit > 2D Sketcher
   • The 2D Workspace - 2D Sketcher panel opens
2. Draw the protonated form of the lauryl ether sulfate anion, as shown in the Figure
   • In the next step we will add the anionic charge, and in a later step we will add the sodium cation separately

 

Note: Alternative to drawing a structure like this, you can typically find a good starting model to import from PubChem or other repositories

Figure 3-2. Adding the negative charge.

3. Click on the Decrease Charge button () in the 2D Sketcher
4. Click on the protonated oxygen to change it to monoanionic
   • A minus charge appears in the sketcher

Figure 3-3. Adding the negative charge.

5. In the bottom of the 2D Sketcher, click Save as New
6. For Input Entry Title input LES_anion
7. Click OK
8. Close the 2D Sketcher panel
   • A new entry is added to entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion titled LES_anion and the structure 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 3-4. All of the atoms selected in the workspace.

9. Select all of the atoms in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed (Several ways to do so: use the button in the Quick Select section of the toolbar, use command+A on Mac or control+A on Windows, or hold shift and click and drag a box around the molecule)

Figure 3-5. Stylizing the structure.

10. To change the visualization of the molecule, go to the Style palette ()
11. Click Apply ball-and-stick representation
    • The style changes from wire to ball-and-stick

Figure 3-6. Minimizing the structure.

Let’s also perform a force field minimization to arrive at an improved starting model:

12. With the atoms all still selected, go to the Build palette ()
13. Click Minimize selected atoms ()
    • The molecule is force-field minimized

Figure 3-7. Adjusting a dihedral.

In this example, our aim is to build a model of a bilayer. To get a tighter, more realistic pack from the structured liquid build, it will be best if the molecule begins a bit more linear, as we expect it to be in the final bilayer. Note that a) this is just a starting model (we will run molecular dynamics later) and b) the structured liquid builder is going to pack the molecule with an initial conformation exactly matching this input

So, let’s manipulate the structure a bit to get a better, more linear starting point. To do so:

14. Select four atoms near any of the sharp bends in the chain, right-click, click Adjust Dihedral and follow the prompts to rotate
    • Alternatively, right-click the middle bond and choose Rotate Dihedral
    • Repeat this until the chain is significantly more linear. Feel free to use the force-field minimization periodically as you go
    • If you’re having trouble with these workspace manipulations, you can always import input_molecules.mae and use the provided structure

Figure 3-8. A more linear LES anion after manually adjusting several dihedrals.

The lauryl ether sulfate entry is now ready for the eventual build. 

Figure 3-9. Creating an empty entry.

We will now prepare the sodium cation entry.

15. Right-click on any empty space in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
16. Click Create New Entry > Create Empty Entry

Figure 3-10. Naming the empty entry.

A prompt appears asking for an Entry title

17. Input sodium_cation and click the green check
    • A new entry is added to the entry list. It 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 by default and is an empty entry containing no structure yet

Figure 3-11. Drawing a sodium cation in the 2D Sketcher.

18. From the main menu, go to Edit > 2D Sketcher
19. Draw a sodium atom
20. Click on the Increase Charge button
21. Click on the atom to change it to monocationic
22. Click Update Entry
23. Close the 2D Sketcher panel
    • A new entry is added to entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion titled sodium_cation and the structure 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 3-12. The stylized sodium cation.

If you wish, follow the above steps to change the style of the atom to ball-and-stick for visualization.

Figure 3-13. Creating an empty entry.

Finally, we will prepare the water entry.

24. Right-click on any empty space in the workspace
25. Click Create New Entry > Create Empty Entry

Figure 3-14. Naming the empty entry.

A prompt appears asking for an Entry title

26. Input water and click the green check
    • A new entry is added to the entry list. It 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 by default and is an empty entry containing no structure yet

Figure 3-15. Drawing a water molecule in the 2D Sketcher.

27. From the main menu, go to Edit > 2D Sketcher
    • The 2D Workspace - 2D Sketcher panel opens
28. Draw a water molecule
29. Click Update Entry
30. Close the 2D Sketcher panel
    • A new entry is added to entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion titled water and the structure 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 3-16. The stylized water molecule.

If you wish, follow the above steps to change the style of the molecule to ball-and-stick for easier visualization.

31. 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 created entries, right-click one and select Group…, name the new group input_molecules

Now we have prepared entries for the three components of our system. We will now proceed to use the Build Structured Liquid panel to prepare our bilayer.

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

Figure 4-1. Selecting LES_anion and opening the Build Structure Liquid 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 LES_anion from 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 > Structure Builders > Structured Liquid
   • The Build Structured Liquid panel opens

Figure 4-2. Importing the surfactant.

3. In the Surfactants section of the panel, click Import from Workspace
   • LES_anion imported appears in the panel
   • An option to Include counter-ion is now available. The panel recognizes that the surfactant is charged

Figure 4-3. Defining the hydrophilic end.

We need to define the hydrophilic and hydrophobic ends of the surfactant for the builder:

4. Next to Hydrophilic end atom indices, click Define
   • The ASL panel opens
5. In the workspacethe 3D display area in the center of the main window, where molecular structures are displayed, select the sulfur atom and the three terminal oxygen atoms
6. Back in the ASL panel, click Selection and then click OK
   • The atom indices are added to the panel which define the hydrophilic end

Figure 4-4. Defining the hydrophobic end.

 

Figure 4-5. Surfactant head-tail vector

7. Next to Hydrophobic end atom indices, click Define
   • The ASL panel opens
8. In the workspacethe 3D display area in the center of the main window, where molecular structures are displayed, select the tail carbon atom and the three terminal hydrogen atoms (be sure to deselect the sulfur and oxygen atoms)
9. Back in the ASL panel, click Selection and then click OK
   • The atom indices are added to the panel which define the hydrophobic end
10. Note that an arrow appears in the workspace that displays the head-tail vector from hydrophilic to hydrophobic atoms.

 

Note: These example ASL selections are good designators of the head and tail, but selecting only the S or C atom would also be sufficient, or other combinations to generally indicate which end is hydrophilic and which is hydrophobic.  Not all of the atoms need to be included in the hydrophilic and hydrophobic selection.

Figure 4-6. Importing the cation.

11. Keep the panel open, and back in the 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 and includethe entry is represented in the Workspace, the circle in the In column is blue sodium_cation
12. Back in the panel, next to Include counter-ion, click Import from Workspace
    • sodium_cation imported appears in the panel

Figure 4-7. Importing the solvent.

13. Keep the panel open, and back in the 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 and includethe entry is represented in the Workspace, the circle in the In column is blue water
14. Back in the panel, in the Solvents section, click Import from Workspace
    • water imported appears in the panel

Figure 4-8. Setting up the bilayer model and running the job.

15. For Model type maintain Bilayer
    • Several Model type options are available for packing your structure liquid
16. For Cell lengths change c to 80.00
    • This will generate a system with a reasonable number of atoms and a water content that facilitates a stable bilayer
    • In practice, given the phase space for this example, finding the right water content to derive a bilayer system is non-trivial. Another building tool that can be useful is the Remove Molecules from System panel
    • The bilayer will be built on the ab plane, so the c length will be directly related to the amount of solvent
17. Change the Packing efficiency factor to 0.6
    • See further discussion of this parameter below
18. Change the Job name to structured_liquid_SLES
19. Adjust the job settings () as needed
    • This job requires a CPU host. The job can be completed in about 15 minutes
20. If you would prefer not to run the job, import Section_04 > structured_liquid_SLES > structured_liquid_SLES_system-out.cms from the provided tutorial files. Otherwise, click Run
    • If a Question dialog box appears, ignore the warning and click Continue
21. Close the Build Structured Liquid panel

Figure 4-9. Output of the build.

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

22. 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
    • The box dimensions might be different than what was originally set in the Build Structured Liquid panel. This is done to avoid overlaps between the atoms while they are packed in this specific structure. However, this will not affect the results of our calculations.

Figure 4-10. Using the WAM Button.

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

Figure 4-11. Setting up the first two steps of the MD Multistage workflow.

24. Ensure that Project Table (1 selected entry) is chosen for Use structures from
25. Maintain the first stage as a Brownian Minimization with the default settings
26. Click Append Stage
27. Change the Stage type to Molecular Dynamics
28. Set the Simulation time to 0.1 ns, Ensemble class to NVT, the Temperature to 10.0 K and the Time step to 1.0 fs

 

These first two steps slowly introduce dynamics

Figure 4-12. Setting up the third step of the MD Multistage workflow.

29. Click Append Stage
    • A 3rd stage appears
30. Change the Stage type to Molecular Dynamics
31. Set the Simulation time to 20 ns, Recording interval to 40, Ensemble class to NPγT, and the Surface tension to 3380

 

This step with constant surface tension (γ) allows the x,y box vectors to change together, independently of z. This constraint, along with hydrophobic interactions at the chosen composition, drives the system towards a stable bilayer configuration. The surface tension value is based on literature precedent.

 

For further details about the various stages that can be added to a MD Multistage Workflow, see the help documentation and the Disordered System Building and Molecular Dynamics Multistage Workflows tutorial.

32. Change the Job name to multistage_simulation_SLES
33. Adjust the job settings () as needed
    • This job requires a GPU host. The job can be completed in about 3 hours on a single GPU host
34. If you would prefer not to run the job, import Section_04 > multistage_simulation_SLES > multistage_simulation_SLES-out.cms from the provided tutorial files. Otherwise, click Run
35. 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 4-13. The bilayer after the MD Multistage workflow.

When the job finishes or after importing, a new entry is added to the entry list titled structured_liquid_SLES in a new entry group.

Feel free to view the trajectory () and visualize the box. In the next section we will change the style.

Figure 5-1. Selecting the water molecules.

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 new structured_liquid_SLES entry

For ease of visualization, let’s hide the water molecules and change the style of the sulfur atoms:

2. From the main menu, go to Select > Solvent
   • The water molecules are selected in the workspace

Figure 5-2. Hiding the water molecules.

3. Go to the Style palette ()
4. Click Undisplay selected atoms
   • The water molecules are no longer shown

Figure 5-3. Defining the ASL to select the sulfur atoms.

5. From the main menu, go to Select > Define
   • The Atom Selection panel opens
6. In the Atom tab, choose Element, then choose S and click Add
   • (atom.ele S) appears in the ASL window

Figure 5-4. The stylized bilayer.

7. Click OK
   • The panel closes and the 244 sulfur atoms are selected in the workspace
8. Go to the Style palette ()
9. Click on Apply CPK Representation
   • The sulfur atoms are changed to CPK representation, clarifying our view of the bilayer
10. Clear the workspace selection by clicking on any blank space or using the Clear selection button ()

 

Note: Recall that the cell is defined by periodic boundary conditions (PBCs). If you are having trouble visualizing the bilayer, feel free to use the Periodic Structure Tools to view additional extents. If doing so, Revert to ASU before proceeding.

Figure 5-5. Selecting and including the entry and opening the panel.

11. With the structured_liquid_SLES entry 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, go to Tasks > Materials > Classical Mechanics > Trajectory Analysis > Surfactant Tilt Calculations
    • The Surfactant Tilt Calculation panel opens

Figure 5-6. Loading the entry into the panel.

12. Click Load from Workspace
    • structured_liquid_SL… appears next to the button
    • The Trajectory Frames button is ungreyed and the frames and simulation time are shown
    • A plane appears in the workspace

Figure 5-7. Selecting the surfactant.

13. Maintain the Trajectory Frames
    • You can use this button to designate the calculation to only be performed on a subset of the trajectory
14. Maintain the default Plane selector option as Crystal vector c
    • This should be the plane that is perpendicular to the surfactant chains
15. In the Head/Tail selector section of the panel, for Surfactant choose C18H37O7S #:244 which is associated with the LES anions

Figure 5-8. Selecting the hydrophilic end atoms.

16. For Representative hydrophilic end atom indices, check Pick
    • The workspace adjusts to show a single surfactant molecule, which will be representative of all of the molecules across all of the trajectory frames
17. In the workspacethe 3D display area in the center of the main window, where molecular structures are displayed, select the sulfur atom and the three terminal oxygen atoms
    • The indices appear in the panel

Figure 5-9. Selecting the hydrophobic end atoms.

18. For Representative hydrophobic end atom indices, check Pick
19. In the workspacethe 3D display area in the center of the main window, where molecular structures are displayed, select the last carbon atom in the chain
    • A vector appears designating the angle from the plane to the carbon; this is how the vector will be defined for all molecules of the same type  in order to calculate the tilt and rotational angles
    • The index of the carbon atom appears in the panel

Figure 5-10. Naming and running the job.

20. Change the Job name to surfactant_tilt_SLES
21. Adjust the job settings () as needed
    • This job requires a CPU host. The job can be completed in about 2 minutes
22. Click Run
    • If a warning appears about the picking state, click OK or continue
23. Close the Surfactant Tilt Calculation panel
    • Click OK if a message appears about changing modes

Figure 5-11. Using the WAM button to access the results panel.

When the job finishes, a new entry is added to the entry list, again titled structured_liquid_SLES in a new entry group which now contains the surfactant tile data.

24. Use the WAM () button to access the Surfactant Tilt Viewer panel
    • Alternatively, go to Tasks > Materials > Classical Mechanics > Trajectory Analysis > Surfactant Tilt Results and click Load Data from Workspace

Figure 5-12. The viewer panel after opening and symmetrizing.

The viewer panel has three plots: Time series of tilt and rotational angles versus time, Tilt angle distribution and Rotational angle distribution

25. Check Symmetric tilt angle
    • The panel default includes tilt angles to 180º. Ticking this box standardizes the tilt angles from 0-90º

 

See the bottom of the viewer panel for detailed analysis. You can:

• View the average tilt and rotational angles as well as their time series and distribution standard deviations
• View data for specific atoms selected in the workspace
• Change the trajectory range of the analysis (either input times in the Start time and End time boxes or slide the dashed bars in the Time series graph)
• Export the data for further analysis

Figure 5-13. The viewer panel after changing the analysis window.

In this instance, the simulation does not look completely equilibrated until at least the last half of the trajectory - depending on our goals, analysis of the time series indicates that we should consider a longer production simulation.

Nonetheless, we can adjust the analysis to hone in on the last half of the trajectory:

26. Click and drag the left dashed slider to ~10 ns
    • This will change the analysis to only the ~10-20 ns range
    • The data at the bottom of the panel updates, as well as the Distribution plots

 

Analysis allows for a few initial conclusions to be drawn:

• The average tilt angle of ~30º as well as the relatively broad distribution indicates that the surfactants are fairly disordered
• The rotational angle becomes more uniform as the slider moves forward (try toggling the range and viewing the updated plot). Again, this indicates that the system is not fully equilibrated earlier in the trajectory, and may need even more time. Likely the two peaks in the Rotational angle plot are a remnant of order from the initial configuration and we are viewing the slow transition towards the more uniform distribution at the end of the trajectory

 

Proceed to explore the analysis capabilities as you wish.

 

27. Afterwards, close the Surfactant Tilt Viewer panel

Figure 6-1. Selecting the bilayer, opening the panel and loading the 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 structured_liquid_SLES entry output from the MD simulation
   • Do not select the entry from the surfactant tilt output
2. Go to Tasks > Materials > Classical Mechanics > Trajectory Analysis > Trajectory Electrostatic Potential Analysis Calculations
   • The Trajectory Electrostatic Potential Calculation panel opens
3. Click Load from Workspace
   • The panel is populated, matching the Figure

Figure 6-2. Selecting the bilayer, opening the panel and loading the trajectory.

4. Click Trajectory Frames
   • The Trajectory Frames panel opens
5. Set the panel to intake Frames 400 - 500 with a Step size of 1
   • From our analysis of the surfactant tilt, it appears the system is reasonably equilibrated in the final 20% of the trajectory
6. Click OK
   • Back in the main panel, the trajectory frames updates to indicate 101 frames, 16.00-20.00 ns

Figure 6-3. Defining the solvent.

7. Maintain the default Mode, Slice thickness, Solvent relative permittivity and Axis
8. In the Solvent atoms section, use the button to choose Waters
   • 4188 atoms selected; water appears in the section of the panel
   • The solvent must be defined so that the trajectory can be centered on the solvent. The center point in the z-direction is used as the reference point for the calculations (z = 0 in the upcoming output plots)
   • If the solvent is not available in the preset dropdown, you can use the Pick option to interact with the workspacethe 3D display area in the center of the main window, where molecular structures are displayed

Figure 6-4. Naming and running the job.

9. Change the Job name to trajectory_esp_analysis_SLES
10. Adjust the job settings () as needed
    • This job requires a CPU host. The job can be completed in about 1 minute
11. Click Run
12. Close the Trajectory Electrostatic Potential Analysis panel

Figure 6-5. Using the WAM button to access the results panel.

When the job finishes, a new entry is added to the entry list, again titled structured_liquid_SLES in a new entry group which now contains the charge density and electrostatic potential data.

13. Use the WAM () button to access the Trajectory Electrostatic Potential Analysis Viewer panel
    • Alternatively, go to Tasks > Materials > Classical Mechanics > Trajectory Analysis > Trajectory Electrostatic Potential Analysis Results and click Load Data from Workspace

Figure 6-6. Charge density plot.

The first Plot shown is Charge density (C/cm³).

The plot shows charge density as a function of distance from the center of the solvent in the z dimension (perpendicular to the bilayer). z=0 corresponds to the center of the bulk solution (based on the selected solvent in the calculations panel) which is filled with positively charged sodium ions. The plot is approximately symmetric about z=0 since the bilayer geometry is also symmetric. Moving away from z=0 in both directions, the average charge density becomes negative in the region corresponding to the negatively charged sulfate head groups. Proceeding further into the bilayer, the charge becomes slightly positive due to a smaller number of sodium ions that penetrate the bilayer surface. Finally, the charge density becomes zero within the uncharged alkane tails.

Figure 6-7. Electrostatic potential plot.

14. Go to the Electrostatic potential (mV) Plot

The plot shows the electrostatic potential (ESP) along the z dimension, relative to the reference position at z=0. Recall that ESP represents the amount of work needed to move a unit charge from a reference point to a second point within an electric field. This potential accumulates according to the electric field separating the two points. Therefore, the electrostatic potential at the reference point z=0 is, by definition, 0. Moving within the first 5 Å on either side of the reference point, the ESP is greater than 0, indicating that work must be done in order to move a charge from the reference position. ESP reaches a minimum in the region corresponding to the negatively charged sulfate groups. A single positive charge would be quite happy at this position. Finally, the ESP levels off at a negative value in the region of the alkane tails. The negative ESP at the extremes of this plot suggests that the system is not fully equilibrated. Both electrostatic and steric barriers along the way hinder charge diffusion away from the highly charged region around the reference point. It is possible that we have reached an equilibrium balance of these forces. However, longer simulations may allow the ESP profile to evolve further.

15. Close the Trajectory Electrostatic Potential Analysis Viewer

Figure 6-8. An alternative visualization of the bilayer oriented to match the Charge density and Electrostatic potential plots.

A view is provided in the Figure with the cell aligned to the two plots for ease of visualization and analysis.