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/cg_skin.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 CG_skin_tutorial, click Save
   • The project is now named CG_skin_tutorial.prj

Figure 2-3. The entry list after importing the input structures

8. Go to File > Import Structures
9. Navigate to where you downloaded the provided tutorial files (presumably in your working directory), choose Starter_molecules.maegz
10. Click Open
    • A new entry group is added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion containing 6 entries

Note: The CER_24 structure will not be used in this tutorial, but is provided in case there is interest in constructing a pure ceramide bilayer as shown in Badhe et. al J Mol Model (2020) 26:182.

Figure 3-1. Selecting structures.

1. In the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion, includethe entry is represented in the Workspace, the circle in the In column is blue the CER_18 entry and 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 CER_18, CHOL_cholesterol, WF_water, W_water and Palmitic_acid entries.

Figure 3-2.  Setting the component table in the Disordered System Builder.

2. Go to Tasks > Materials > Structure Builders > Disordered System
   • The Disordered System Builder panel opens
   • A Warning may appear. If so, click OK. We will handle the force-field typing in a later step
3. Change the Initial state to Amorphous
   • This will place molecules randomly in the box without overlaps.
4. Change the Number of molecules to 2333
5. For Molecules for each Component, input the following (as shown in the Figure)
   • CER_18 = 142
   • CHOL_cholesterol = 100
   • WF_water = 200
   • W_water = 1800
   • Palmitic_acid = 91
6. Go to the Disorder tab

Note: This particular composition is adapted from Badhe et. al  J Mol Model (2020) 26:182. We recommend using a commonly employed option in the Martini force field of two types of water particles (W and WF) to reduce the chance that the solvent particles might freeze. Typically, 10% of all water molecules are represented by anti-freeze particles (WF).

Figure 3-3. Setting the Disorder tab and running the job.

7. Uncheck Color molecules by component
8. Change the Job name to disordered_system_skin_components
9. Adjust the job settings as needed. This job requires a CPU host. The job can be completed in about 10 minutes.
10. If you would like to run the job yourself, click Run. Otherwise, go to File > Import Structures, navigate to the provided tutorial files and OpenSection_03 > disordered_system_skin_components > disordered_system_skin_components_amorphous.maegz
11. Close the Disordered System Builder panel.

Figure 3-4. Selecting and including the output structure.

12. When the job is finished or after importing, 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 disordered_system_skin_components_all_components_amorphous

Figure 3-5. Opening the Coarse Grained Force Field Assignment panel.

Before running the MD simulation, a necessary step is to perform the force field assignment.

13. Ensure that disordered_system_skin_components_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 and go to Tasks > Materials > Classical Mechanics > Coarse Grain Models > Coarse-Grained Force Field Assignment
    • The Coarse Grained Force Field Assignment panel opens.

Figure 3-6. Assigning force field parameters.

14. Choose Martini_skin from the dropdown options in the Import force field option
    • If Martini_skin is not available in the Import force field dropdown, revisit the end of Section 2
15. Click Import.
16. Click OK on the warning message to continue enumerating types
    • All of the Martini force field parameters are automatically assigned to all of the particles
17. Click Run to finalize the force field assignment
18. Click Continue if a pop-up message appears
    • This job takes a few seconds
    • A banner appears when the job has been incorporated
    • A new group titled Coarse-Grained Force Field Assignment (1) with a new entry titled disordered_system_skin_components_all_components_amorphous is added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion. It is 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 in the workspace.  

Note: The force field parameters for ceramide (CER_18) and palmitic acid have been assigned for each CG particle as described in Badhe et. al J Mol Model (2020) 26:182 and the bead types for cholesterol (CHOL), water (W_water) and anti-freeze water (WF_water) are taken from the Martini force field as described in the Selecting Martini Parameters documentation page.

Figure 3-7. Setting up the stages for the MD Multistage Workflow.

19. In the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion, select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries and includethe entry is represented in the Workspace, the circle in the In column is blue the new entry disordered_system_skin_components_all_components_amorphous
20. Use the WAM (workflow action menu) button () to access the MD Multistage Workflow panel
    • Alternatively, go to Tasks > Materials > Classical Mechanics > MD Simulations > MD Multistage Workflow
21. Check Relaxation protocol and maintain the default Martini protocol for equilibration
22. For (7) Stage Type select Martini Molecular Dynamics
23. Set Simulation time to 100 ns
24. Set trajectory Recording interval to 500 ps and Energy Recording interval to 50 ps
25. Maintain NPT Ensemble class.
26. Change Temperature to 310 K
27. Click Advanced Options

Figure 3-8. Setting up advanced options.

28. In the Ensemble tab, Maintain the Langevin for both Thermostat and Barostat
29. Set the Thermostat Relaxation time to 1.0 ps
30. Set the Barostat Relaxation time to 12.0 ps
31. Choose Semi-isotropic pressure coupling in the Coupling style dropdown options
32. Click Apply and then OK to close the window

Note: Generally, lower values of time constants for thermostats and barostats allow for faster equilibration. However, finding the right balance is crucial to avoid high-frequency fluctuations or run-off. Additionally, a semi-isotropic or anisotropic pressure coupling is typically recommended for membrane or bilayer simulations.

Figure 3-9. Running the MD Multistage Workflow.

33. Set Time step to 5.0 fs
    • The time step should be smaller than the lowest time constant of either the thermostat or the barostat. It should be small enough to accurately capture the dynamics while being large enough to avoid interference with the thermostat/barostat’s operation.
34. Change the job name to multistage_simulation_disordered_skin_components
35. Adjust the job settings   as needed.
    • This job requires a GPU Host and takes ~2 hours to complete.
36. If you would prefer not to run the job, import Section_03 > multistage_simulation_disordered_skin_components > multistage_simulation_disordered_skin_components-out.cms from the provided tutorial files via File > Import Structures. Otherwise, click Run.
37. Close the MD Multistage Workflow panel.

Figure 3-10. The output after running or importing the job.

38. In the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion, select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries and includethe entry is represented in the Workspace, the circle in the In column is blue the output from the previous step disordered_system_skin_components_all_components_amorphous

Proceed to visualize the trajectory if you are interested. For a reminder on how to visualize trajectories, see the Disordered System Building and Molecular Dynamics Multistage Workflows or Building, Equilibrating and Analyzing Amorphous Polymers tutorials.

Note: Recall that the simulation employs periodic boundary conditions (PBCs). In this case, at a first glance, the bilayer may look separate, but actually the skin components form a neatly stacked bilayer. We will perform cell manipulation and structural analysis in Section 5.

Figure 4-1. Opening the Build Structured 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 the CER_18 entry in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion in the Starter_molecules group.
2. Go to Tasks > Materials > Structure Builders > Structured Liquid
   • The Build Structured Liquid panel opens

Figure 4-2. Importing the ceramide molecule.

3. In the Surfactants section of the panel, click Import from Workspace
   • CER_18 imported appears in the panel
4. Check Number of molecules  and input 71
   • The number of molecules we input here corresponds to each leaflet of the bilayer. Since we want the bilayer composition to consist of 142 ceramide molecules, we use half of that for each leaflet.

Figure 4-3. Selecting hydrophilic atom indices.

5. For selecting the Hydrophilic end atom indices click Define
   • The ASL panel opens
6. In the workspace select the CG beads as shown in the figure and click Selection
   • Atom numbers 1, 2 and 3 are selected as the hydrophilic end atom indices.
7. Click OK

Figure 4-4. Selecting hydrophobic end atom indices.

8. For selecting the Hydrophobic end atom indices click Define
   • The ASL panel opens
9. In the workspace select the CG beads as shown in the figure and click Selection
   • Atoms numbered 7 and 11 are selected as the hydrophobic end atom indices.
10. Click OK

Figure 4-5. Arrow pointing from the hydrophilic end to the hydrophobic end.

A vector appears in the workspace that displays the head-tail vector from hydrophilic to hydrophobic particles for the ceramide molecule.

Figure 4-6. Importing the Cholesterol molecule.

11. Keeping the panel open, 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 CHOL_cholesterol entry from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
12. Click Add at the bottom of the Surfactants section of the panel
    • This will add an option to add another molecule to be used for building the bilayer
13. In the Surfactants section of the panel, click Import from Workspace
    • CHOL_cholesterol imported appears in the panel
14. Check Number of molecules and input 50
    • Again, targeting a bilayer composition of 100 cholesterol molecules, we use half of that for each leaflet.

Figure 4-7. Selecting hydrophilic atom indices.

15. For selecting the Hydrophilic end atom indices click Define
    • The ASL panel opens
16. In the workspace select the CG beads as shown in the figure and click Select
    • Atom number 1 is selected as the hydrophilic end atom index.
17. Click OK

Figure 4-8. Selecting hydrophobic atom indices.

18. Repeat steps 15-17 for selecting atom number 8 of the cholesterol molecule as the Hydrophilic end atom indices

Figure 4-9. Importing palmitic acid.

19. Keeping the panel open, 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 Palmitic_acid entry from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
20. Click Add at the bottom of the Surfactants section of the panel
    • This will add an option to add another molecule to be used for building the bilayer.
21. In the Surfactants section of the panel, click Import from Workspace
    • Palmitic_acid imported appears in the panel
22. Check Number of molecules and input 45

Figure 4-10. Selecting hydrophilic atom indices.

23. For selecting the Hydrophobic end atom indices click Define
    • The ASL panel opens
24. In the workspace select the CG beads as shown in the figure and click Select
    • Atom number 1 is selected as the hydrophilic end atom index.
25. Click OK

Figure 4-11. Selecting hydrophobic atom indices.

26. Repeat steps 23-25 for selecting atom number 5 of the Palmitic acid molecule as the Hydrophobic end atom indices.

We have selected the components required to build the two leaflets of the bilayer. Next we will import solvent particles to complete the structure.

Figure 4-12. Importing water.

27. Keeping the panel open, 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 W_water entry in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.
28. In the Solvents section of the panel, click Import from Workspace
    • W_water imported appears in the panel
29. Check Number of molecules and input 900

Figure 4-13. Importing anti-freeze water.

30. Click Add at the bottom of the Solvents section of the panel
    • This will add an option to add another solvent
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 and includethe entry is represented in the Workspace, the circle in the In column is blue the WF_water entry in the entry list
32. In the Solvents section of the panel, click Import from Workspace
    • WF_water imported appears in the panel
33. Check Number of molecules and input 100

Figure 4-14. Setting up the bilayer model and running the job.

34. For Model type maintain Bilayer
    • Several Model type options are available for packing your structure liquid.
35. For Cell lengths change a,b and c to 100.0 Å
36. Select Local installation and choose Martini_skin for Coarse-grained force field
    • This will prepare the system for MD simulation by assigning force field parameters.
37. Click Update Densities
    • The panel prints the total density of the system. This allows us to ensure that the initial configuration is a relatively low density. Upon equilibration in later steps, the system will reach an equilibrium density.
38. Uncheck Attempt to prevent ring-spears
39. Change Job name to structured_liquid_skin_components
40. Adjust the job settings as needed
    • This job requires a CPU Host and takes ~10 minutes to complete.
41. 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_04 > structured_liquid_skin_components > structured_liquid_skin_components-out.cms
42. Click Continue for any warning message that appears.
43. Close the Build Structured Liquid panel

Figure 4.15. Opening the MD multistage workflow panel.

44. After running the job or importing, a new entry titled structured_liquid_skin_components appears in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion

Recall that this structure has not yet been equilibrated by molecular dynamics (MD), and is just a starting model to now submit for an MD simulation. Of course, unlike the input system used in Section 3, this system is pre-formed, which should result in rapid equilibration to the expected bilayer structure. Also note that the box dimensions might be different than the original settings in the Build Structured Liquid panel. This fine-tuning is done to avoid overlaps between the atoms while they are packed in this specific structure. This will not affect the results of our calculations.

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

Figure 4-16. Setting up the MD multistage panel.

46. Repeat steps 20-31 from Section 3 and change the Simulation time to 20 ns.

Figure 4-17. Running MD Multistage workflow.

47. Set Time step to 5.0 fs
48. Change the job name to multistage_simulation_structured_skin_components
49. Adjust the job settings   as needed.
    • This job requires a GPU Host and takes ~ 30 minutes to complete.
50. If you would like to run the job yourself, click Run. Otherwise, go to File > Import Structures, navigate to the provided tutorial files and OpenSection_04 > multistage_simulation_structured_skin_components > multistage_simulation_structured_skin_components-out.cms
51. Close the MD Multistage Workflow panel

Figure 4-18. Output from the MD multistage workflow.

52. 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 the output from the previous step structured_liquid_skin_components

Proceed to visualize the trajectory if you are interested. For a reminder on how to visualize trajectories, see the Disordered System Building and Molecular Dynamics Multistage Workflows or Building, Equilibrating and Analyzing Amorphous Polymers tutorials.

Figure 5-1. Duplicating the entry.

Before performing the analysis, we will modify the output structure in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

For the analysis stage, we will proceed with the output from Section 4, but feel free to repeat the analysis with the output from Section 3 as well if you are interested.

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 output from the second MD simulation structured_liquid_skin_components
2. Right click on the entry and select Duplicate > In Place
   • This will create a duplicate entry just below the original entry
3. Rename the entry to structured_liquid_skin_components_duplicate

Figure 5-2. Manipulating the cell.

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 duplicate entry structured_liquid_skin_components_duplicate
5. Go to Tasks > Materials > Tools > Manipulate Cell
   • The Manipulate Cell panel opens
6. For Manipulation, choose Translate to first cell
   • This manipulation will translate the atoms of the structure, such that all the fractional coordinates with respect to the chosen axes (in this case all) are within the range (0,1). Only the atoms that are outside the first cell are translated.
7. Click Run
   • Click Continue for the warning message
8. Close the Manipulate Cell panel
9. A new entry named structured_liquid_skin_components_duplicate is created in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.

Note: This entry does not contain the trajectory data.It is merely a snapshot of the last frame of the trajectory from the original entry.

Figure 5-3. Opening the density profile panel.

10. Select and include the output from the cell manipulation structured_liquid_skin_components_duplicate
11. Go to Tasks > Materials > Tools > Density Profile
    • The Density Profile panel opens

Figure 5-4. Density profile.

12. For Axis, choose Z-Axis
13. Click Analyze Workspace
    • The panel updates with a plot of the density profile in the Z-direction.
    • The density profile has three main features - a low density region which corresponds to water particles, high density shoulders which correspond to the bilayer components’ tail particles, and a valley in between which denotes the gap between the bilayer leaflets.
14. Go to the Cross Section tab  

Figure 5-5. Analyzing the cross section density.

We can use the Cross Section tool to look at the density for specific planes

15. Use the arrows or the layer input box to shift the plane (shown in the workspace in red)

Feel free to explore other cross sections in the box by navigating with the arrows

Figure 5-6. Opening the surfactant tilt calculations panel.

Next we will calculate tilt angles of the ceramide molecules with respect to the bilayer surface.

16. 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 from the second MD Multistage Workflow structured_liquid_skin_components
17. Go to Tasks > Materials > Classical Mechanics > Trajectory Analysis > Surfactant Tilt Calculations
    • The Surfactant Tilt Calculations panel opens

If you are unfamiliar with the Surfactant Tilt workflow, please feel free to visit the Calculating Surfactant Tilt and Electrostatic Potential of a Bilayer System tutorial for a more comprehensive introduction.

Figure 5-7. Setting up trajectory frames for the calculation.

18. Click Load from Workspace
    • structured_liquid_sk… appears in the panel
19. Click Trajectory Frames
20. Input 100 for the starting frame
    • In this case, we choose the last 100 frames  to sample statistically averaged data from the second half of the simulation
21. Click OK
    • The Trajectory Frames window closes

Figure 5-8. Defining the plane and selecting the Ceramide molecule.

22. In the Plane selector section of the panel, choose c as the Crystal vector
    • A plane showing the surface normal to the z-axis appears on the workspace
    • Alternatively, there is an option to define the plane using any 3 atoms of choice
23. In the Head/Tail selector section, select (CER_H1)(CER_H2)...(CER_TB4) #:142 as the Surfactant
    • This specifies which surfactant to perform the surfactant tilt calculation for

Figure 5-9. Selecting the hydrophilic end atom index.

24. For Representative hydrophilic end atom indices choose Pick
    • A single ceramide molecule is shown in the workspace as the representative molecule
25. Select the red bead at the center
    • A plane appears in the workspace indicating the plane of the bead
    • In the panel the number is updated to 2892 which is the particle ID of the bead

Figure 5-10. Selecting the hydrophobic end atom indices.

26. For Representative hydrophobic end atom indices choose Pick
    • The same ceramide molecule is shown in the workspace as the representative molecule.
27. Select the green and violet beads.
    • An arrow appears in the workspace indicating the vector from the hydrophilic to the hydrophobic end
    • In the panel, the input is updated to 2897,2901 which are the particle IDs

Figure 5-11. Running the surfactant tilt calculation job.

28. Change the Job name to surfactant_tilt_skin_bilayer
29. Adjust the job settings as needed
    • This job requires a CPU Host and takes ~2 minutes to complete.
30. If you would prefer not to run the job, import Section_05 > surfactant_tilt_skin_bilayer > surfactant_skin_bilayer-out.cms provided tutorial files via File > Import Structures. Otherwise, click Run.
31. Click OK if any warning message appears
32. Close the Surfactant Tilt Calculations panel

Figure 5-12. Opening the surfactant tilt results panel.

33. Once the job finishes running or after importing, a new entry structured_liquid_skin_components is 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 in the workspace.
34. Use the WAM button to access the Surfactant Tilt Results panel
    • Alternatively, go to Tasks > Materials > Classical Mechanics > Trajectory Analysis > Surfactant Tilt Results
    • The Surfactant Tilt Results panel opens

Figure 5-13. Surfactant tilt results.

This panel shows the tilt angle distribution and the rotational angle distribution using the trajectory. The bottom of the panel shows statistics for the tilt angle and rotational angle

35. Choose Symmetric tilt angle option
    • Since we want to calculate the average tilt angle for a bilayer, it is recommended to use this option. This will treat molecules with same tilt angles but in opposite directions as symmetric. The average tilt angle is around 23.3°.

You can move the sliding bars in the plot to change the data used for generating the distributions

Feel free to explore other options in the panel for further analysis

Figure 5-14. Setting up the Membrane Analysis panel.

Now we will run a short analysis calculation to estimate the area per lipid and thickness of the bilayer.

36. 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 from the second MD simulation structured_liquid_skin_components
37. Go to Tasks > Materials > Classical Mechanics > Trajectory Analysis > Membrane Analysis Calculations
    • The Membrane Analysis panel opens
38. Click Load from Workspace
    • The system is loaded into the panel, the number of frames are shown
    • The trajectory frames for the analysis calculation can be chosen, the default is the full trajectory
39. Ensure the option for Thickness and area per lipid is selected
    • The number of selected atoms and the ASL should update
    • You can highlight the hydrophilic atoms in the workspace

Figure 5-15. Running the Membrane Analysis calculation.

40. Go to the Leaflet Detection tab
41. Select Use lipid orientation
42. For the atoms selected enter atom.name CER_H1 OR atom.name FA_HE1 OR atom.name CHOL_1
43. Set the Distance cutoff to 25
44. Change the Job name to membrane_analysis_structured_skin
45. Adjust the job settings as needed
    • This job requires a GPU subhost for the analysis of the MD simulation. It can be completed in about 5 minutes.
46. If you would like to run the job yourself click Run, otherwise proceed with the provided files
47. Close the Membrane Analysis panel

Figure 5-16. Viewing the Membrane Analysis results.

48. Import the provided results from the zip file via File > Import Structures: Section_05 > membrane_analysis_structued_skin > membrane_analysis_structured_skin-out.maegz
49. Use the WAM (workflow action menu) button () to open the Membrane Analysis Viewer panel
    • Alternatively, access the panel via Tasks > Materials > Classical Mechanics > Trajectory Analysis > Membrane Analysis Results
50. Click Load from workspace to import the results
51. Have a look at the system information in the Summary tab
52. Explore the other tabs and close the Membrane Analysis Viewer panel once finished