1. Double-click the Materials Science icon
   • (No icon? See Starting Maestro)

Figure 2-1. Change Working Directory option.

2. Go to File > Change Working Directory
3. Find your directory, and click Choose
4. Pre-generated input and results files are included for running jobs or examining output. Download the zip file here: schrodinger.com/sites/default/files/s3/release/current/Tutorials/zip/viscosity.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 viscosity_tutorial, click Save
   • The project is now named viscosity_tutorial.prj

Figure 3-1. Drawing and saving hexane.

1. From the main menu, go to Edit > 2D Sketcher
   • The 2D Sketcher panel opens

 

For a complete overview of the sketcher panel, see the 2D Sketcher Panel documentation.

2. Draw a hexane molecule (C₆H₁₄)
3. Click Save as New
4. For Input Entry Title write hexane
5. Click OK
   • Behind the 2D Sketcher in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed and entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion, the hexane molecule has been added

Figure 3-2. Drawing and saving heptane.

6. Keep the 2D Sketcher open and add one carbon to the chain to draw heptane
7. Click Save as New
   • Be sure to not click Update Entry, as doing so will overwrite the hexane entry
8. For Input Entry Title write heptane
9. Click OK
   • Behind the 2D Sketcher in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed and entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion, the heptane molecule has been added
10. Repeat Steps 6-9 for octane, nonane and decane, such that you have created 5 new entries
11. After clicking OK for decane, close the 2D Sketcher
12. If necessary, reorder your entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion by clicking and dragging the entries

Figure 3-3. Including all five alkanes.

13. To visualize all of the molecules in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed simultaneously, includethe entry is represented in the Workspace, the circle in the In column is blue all 5 entries (hold Shift + fill the Includethe entry is represented in the Workspace, the circle in the In column is blue circle for all five molecules)
    • The molecules appear stacked in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed

Figure 3-4. Tiling the entries.

14. Using the Workspace Configuration Panel button (), choose Tile
    • The five alkanes are tiled in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed

Figure 3-5. Stylizing the tiled entries.

15. Click on the Style () palette in the toolbar and choose Apply ball-and-stick representation
    • The five tiled alkanes are stylized to ball-and-stick representation

Figure 4-1. Selecting all entries and opening the Disordered System Builder.

1. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries all five entries from the entry list a simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion(Shift + Click on all 5 rows)
2. Go to Tasks > Materials > Structure Builders > Disordered System
   • The Disordered System Builder panel opens

Figure 4-2. Components tab.

The Disordered System Builder can be used to create a heterogeneous cell containing many components. Here, we wish to prepare five homogeneous cells, one for each component. To do so:

3. Ensure that for Use structures from, Project Table (5 selected entries) is chosen from the dropdown
   • You should see all five molecules listed as components in the panel
4. For Number of Molecules, input 1000
   • This will be the total number of molecules in each cell
   • You can ignore the mixture in the table below, we are going to obviate that specification momentarily

Figure 4-3. Cells tab.

5. Go to the Cells tab
6. Uncheck All components
   • This avoids the construction of the mixed cell
7. Check Homogeneous cell of each component
   • This instructs the builder to prepare the homogeneous cells instead
8. For Initial state, select Tangled chain
9. Change the Job name to disordered_system_alkanes
10. This job takes ~10-20 minutes on a CPU Host. If you would like to run the job yourself, adjust your Job settings as needed and click Run.

If you would prefer to proceed with pre-generated structures, close the Disordered System Builder and import the amorphous cells via File > Import Structures. Navigate to where you downloaded the tutorial files and choose the Section_04 > disordered_system_alkanes_componentN_system-out.cms file where N=1-5.

Figure 4-4. The amorphous cells tiled in the workspace.

When the job is complete (or after importing), five new entry groups are added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.

Optionally, as before, we can view all of the systems simultaneously by including the five outputs and tiling them in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

Feel free to stylize as well. Herein, we will use ball-and-stick representation and element coloring.

Note: In this system, OPLS force fields were used in the system creation but machine Learning Force Fields (MLFF) are available as an alternative to OPLS force fields in the preparation process. Additional information regarding MLFF can be found in the help documentation or on our website.

Figure 5-1. Selecting the five 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 all five new entries from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion (Shift + Click on all 5 rows)
2. Go to Tasks > Materials > Classical Mechanics > MD Simulations > MD Multistage Workflow
   • The MD Multistage Workflow panel opens

Note: Alternatively, you can directly access the MD Multistage Workflow using the Workflow Action Menu (WAM) button () next to each output from the Disordered System Builder

Figure 5-2. Parameterizing the MD Multistage Workflow.

3. Ensure that Use structures from directs to the 5 entries from Section 4
4. Check the box for Relaxation protocol, with Materials Relaxation selected from the dropdown menu
5. For the 4th stage, change the Stage type to Molecular Dynamics with the following parameters:
   • Simulation time Total: 10 ns
   • Recording interval Trajectory: 40 ps
   • Recording interval Energy: 10 ps
6. Add a 5th stage by clicking Append Stage, and change this stage to Analysis

Figure 5-3. Continue parameterizing the MD Multistage Workflow.

7. Add a 6th stage by clicking Append Stage, and change this stage to Average Cell
8. Add a 7th stage by clicking Append Stage, and change this stage to Molecular Dynamics with the following parameters:
   • Simulation time Total: 10 ns
   • Ensemble class: NVT
   • This additional MD step is in line with best practices for equilibrating a system
9. Change the Job name to multistage_simulation_alkanes

This job takes several hours on a GPU Host. If you would like to run the job yourself, adjust your Job settings as needed and click Run

If you would prefer to proceed with pre-generated structures, you can import the amorphous cells via File > Import Structures. Navigate to where you downloaded the tutorial files and choose the Section_05 > multistage_simulation_alkanes_00N > multistage_simulation_alkanes_00N-out.cms files where N=1-5.

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

 

10. Close the MD Multistage Workflow panel

Figure 5-4. Hexane output from the MD Multistage Workflow.

When the job is complete (or after importing), five new entry groups are added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion. If you ran the job, you can view the trajectories using the trajectory viewer (). If you imported the results, the trajectories are not provided.

As before, feel free to stylize as you wish

Figure 5-5. Hexane Simulation Details in the MS MD Trajectory Analysis panel.

We want to check that each system is at equilibrium, which we can assess by analyzing the densities

11. With the output for hexane (the disordered_system_alkanes_component1_all_components_amorphous entry in the new MD: disordered_system_alkanes_component1_system entry group) 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 > MS MD Trajectory Analysis
    • The MS MD Trajectory Analysis panel opens
12. If you ran the job, click Load from Workspace
    • If you imported the results, you will be prompted to Select Trajectory File. You can use the provided multistage_simulation_alkanes_00N-out.cms files which are associated with the different alkanes
    • The Simulation Details are populated with information about the NPT stage MD run

Figure 5-6. Hexane simulated density.

13. Go to the Bulk Properties tab
14. Change the first property to Density from the dropdown

 

We can see that for hexane, the system has equilibrated to an average density of 0.644 which is in quite good agreement with the experimental density of 0.66. This system is ready for viscosity calculations. Feel free to check each of the alkanes.

 

15. Afterwards, close the MS MD Trajectory Analysis panel

Figure 6-1. Selecting the equilibrated cells and opening the Viscosity 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 all five new equilibrated entries from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion (Shift + Click on all 5 rows)
2. Go to Tasks > Materials > Classical Mechanics > Viscosity > Viscosity Calculations
   • The Viscosity panel opens
3. Change the Simulation time to 10 ns
4. Change the Time step to 2.0 fs

Figure 6-2. Parameterizing the Viscosity panel.

5. Ensure that Use structures from directs to the 5 entries from Section 5
6. Open Advanced MD Options
7. Check Set random number seed
8. Change the Energy group recording interval to 0.006 ps. Make sure to press Enter on your keyboard after updating the input to ensure that the panel updates to read yields 1666667 records
   • In the cells below, we will discuss this parameter and some other best practices for using the Viscosity panel

Figure 6-3. Viscosity panel, Fitting option.

9. Switch to the Fitting option tab
10. Click Advanced Options

Figure 6-4. Viscosity panel, Advanced Options.

11. Check the Calculate viscosity via Einstein-Helfand method box
    • In the Einstein-Helfand method, the viscosity is determined from the ensemble average of the mean square displacement (MSD) of the time integral of the pressure tensors at long tau values
    • Calculating the viscosity two different ways provides extra validation for the computed values
12. Click OK to close the Viscosity - Advanced Options window

Figure 6-5. Naming the job in the Viscosity panel.

13. Change the Job name to viscosity_alkanes
14. This job takes several hours on a CPU (for the master job) and GPU Host (for the simulations), highly depending on your GPU resources. If you would like to run the job yourself, adjust your Job settings as needed and click Run

If you would prefer to proceed with pre-generated results, you can import the viscosity jobs via File > Import Structures. Navigate to where you downloaded the tutorial files and choose any or all of the  Section_06 > viscosity_alkanes-00N > viscosity_alkanes-00N-out.cms files

 

15. Close the Viscosity panel

Figure 6-6. Include and load the viscosity output.

16. Use the WAM button () to open the Viscosity Results panel
    • Alternatively, access the panel via Tasks > Materials > Classical Mechanics > Viscosity > Viscosity Results
    • The Viscosity Viewer panel opens
17. To view the output for any of the alkanes (for example, hexane), include the relevant output from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and click Load data from Workspace
    • The Viscosity Viewer Panel updates to show the output
    • The Shear Viscosity (cP) and Standard deviation of fit (cP) are shown below the results figure
    • The Einstein-Helfand Method can be shown by toggling the Method drop-down menu, the Einstein-Helfand Method will produce a Linear fit
    • Both the Green-Kubo and Einstein-Helfand Method should give a similar result
    • The plot shows the last 80% of the simulation time by default

Figure 6-7. Viscosity results for hexane.

By dragging the blue dashed vertical lines, the fitting region can be manually adjusted, however, finding the best fit region for viscosity is not an exact science. The panel usually makes a pretty good guess at where to fit things but it is not perfect.

 

The coefficient of variation is one way to get the right tau limit. If the coefficient is set, then it will choose the right limit such that the standard deviation is x% of the viscosity at time t.

 

The Green-Kubo Method has two different Fitting methods. The exponential fit is empirical, but has a little bit more of a physical basis to it, while the average fitting method is good for eye-balling noisy data.