Thin Plane Shear

Tutorial Created with Software Release: 2026-1
Topics: Consumer Packaged Goods, Pharmaceutical Formulations, Polymeric Materials
Methodology: All-Atom Molecular Dynamics
Products Used: Desmond, MS Maestro

Tutorial files

1.1 GB
This tutorial is written for use with a 3-button mouse with a scroll wheel.
Words found in the Glossary of Terms are shown like this: Workspacethe 3D display area in the center of the main window, where molecular structures are displayed

 

Tip: You can hover over a glossary term to display its definition. You can click on an image to expand it in the page.
Abstract:

 

In this tutorial, we will calculate the thin plane shear viscosity and friction coefficient for a glycerol/water system at different concentrations and temperatures.

 

Tutorial Content

  1. Introduction to Thin Plane Shear

  1. Creating Projects and Importing Structures

  1. Running Thin Plane Shear Calculations

  1. Analyzing Thin Plane Shear Calculations

  1. Conclusion and References

  1. Glossary of Terms

1. Introduction to Thin Plane Shear

A common configuration used in viscometry is that of fluid flow between two parallel plates of area A, separated in the z-direction by distance Δz. When one or both plates are set in motion at constant velocity in the x-direction, vx, shear forces at the plate/fluid interface transfer momentum to the fluid. Newton suggested the following empiricism to describe the force required to maintain the motion of the plate(s):

Where τxz is the shear stress, which describes the drag force in the x-direction (F) on a unit area (A) perpendicular to the z-direction, and is a proportionality constant known as the viscosity. Fluids for which this relationship holds are called Newtonian fluids. At steady state, we expect the velocity profile to be linear which enables us to write a simple expression for viscosity:

We can also use the drag force to compute the coefficient of friction by dividing the drag force by the force normal to the shearing plane, FN:

To enable application of the above equations, this workflow applies biasing forces to the outermost layers, or slabs, of an input configuration in order to drive them at a constant velocity. We directly measure the force which opposes the motion of these slabs. This workflow is suitable for studying homogeneous systems as well as complex mixtures. While viscosity and coefficient of friction are the two main quantitative outputs, there is also considerable value in visualizing the behavior of solutions under shear.

If your main objective is only to compute viscosity of a homogeneous system whose viscosity is expect to be low (≲100 mPa-s), it may be more accurate to use an equilibrium molecular dynamics (MD) method such as Green-Kubo or Einstein Helfand, as described in the Viscosity tutorial.

In this tutorial, we will study a water/glycerol system at two concentrations and three temperatures. The top and bottom layers of the system will be sheared in the x direction. The viscosity and friction coefficient of the system will be calculated using the Thin Plane Shear calculations panel. The results will be analyzed using the Thin Plane Shear Viewer panel.

The workflow is summarized in the following schematic:

For information on building systems and additional practice running MD simulations, see the Disordered System Building and Molecular Dynamics Multistage Workflows tutorial. For other relevant examples, visit the Viscosity tutorial.

2. Creating Projects and Importing Structures

At the start of the session, change the file path to your chosen Working Directorythe location where files are saved in MS Maestro to make file navigation easier. Each session in MS Maestro begins with a default Scratch Projecta temporary project in which work is not saved, closing a scratch project removes all current work and begins a new scratch project, which is not saved. A MS Maestro project stores all your data and has a .prj extension. A project may contain numerous entries corresponding to imported structures, as well as the output of modeling-related tasks. Once a project is saved, the project is automatically saved each time a change is made.

Structures can be built in MS Maestro or can be imported using File > Import Structures (or drag-and-dropped), and are added to the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and Project Tabledisplays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data. The Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion is located to the left of the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed. The Project Tabledisplays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data can be accessed by Ctrl+T (Cmd+T) or Window > Project Table if you would like to see an expanded view of your project data.

  1. Double-click the Materials Science icon

Figure 2-1. Change Working Directory option.

  1. Go to File > Change Working Directory
  2. Find your directory, and click Choose
  3. 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/thin_shear.zip
  4. 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.

  1. Go to File > Save Project As
  2. Change the File name to thin_shear_tutorial, click Save
    • The project is now named thin_shear_tutorial.prj

Figure 2-3. Importing the starting files.

The input structures are provided and should now be located in your Working Directorythe location where files are saved

  1. Go to File > Import Structures
    • The Import panel opens
  2. Navigate to the tutorial files and select all six files that end in .cms
    • Holding shift will allow all to be selected and opened at once
  3. Click Open
    • The structures are imported

Figure 2-4. The workspace with the imported structures.

First, these systems are built using the Disordered System Builder at two different weight percentages of water to glycerol: 9:91 and 80:20.

 

The 9:91 systems contain 1798 water molecules and 3578 glycerol molecules. The 80:20 system contains 5126 water molecules and 250 glycerol molecules.

 

Second, using the MD Multistage Workflow panel, each system has been relaxed and equilibrated using an NPT MD simulation at three different temperatures: 20°C, 50°C, and 80°C.

 

Third, using the Manipulate Cell panel, a strain cell manipulation was performed by adding 40 Å to the c parameter. This creates 40 Å of vacuum in the z direction.

3. Running Thin Plane Shear Calculations

In this section, we will calculate the thin plane shear viscosity and friction calculation using the Thin Plane Shear panel on the six systems.

Figure 3-1. The starting structure.

  1. With the water09_glycerol91_20C entry 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 entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion, go to Tasks > Materials > Classical Mechanics > Thin Place Shear > Thin Plane Shear Calculations

This panel allows you to calculate the thin plane shear viscosity and friction coefficient. Let’s explore the panel options.

Plane selection options: Specifies the atoms that will be selected in the shearing slab. There are two different options for atom selection.

Show selected slabs in Workspace box: This option displays the shearing slabs in the workspace using a different color and nine large spheres. The shearing slabs are being moved by defining nine atoms in each shearing slab. The nine atoms are being pulled in the x-direction and the other atoms in the slab are forced to follow by harmonic restraints. The slab definition will cut through molecular bonds. Due to this procedure, it is important that the system contains enough vacuum in the z-direction and the surface is running perpendicular to the xy-plane. The number of atoms in each slab will be forced by the workflow to be equal. The input system should be consistent in the density of molecules in the two slab regions.

Shear velocity: The velocity of each of the slabs.

Normal pressure: The pressure of the simulation.

Simulation time: The desired time and time step of the simulation.

Temperature: The temperature to be used in the simulation, in kelvin.

Set random number seed: Select this option to specify a random seed to be used in the simulation.

Trajectory recording interval: Set the recording interval for saving points on the trajectory, in ps. This is the amount of time between frames in the trajectory.

For detailed information about the various parameters in the panel, see the help documentation.

 

 

Figure 3-2. The Thin Plane Shear panel.

  1. Ensure that Use structures from shows Workspace (included entry)
  2. Select atoms within 15 Å
  3. Set the Temperature to 293 K
    • This MD simulation was performed at 293 K (20°C) so the thin plane shear calculation needs to be performed at the same temperature

Note: The shear velocity is the velocity of each of the slabs. The top slab is moved at +0.0125 Ang/ps and the bottom slab at -0.0125 Ang/ps.

Note: For best practices, we recommend keeping the normal pressure as 1.2 bar (which is default), to ensure that the slabs remain stable during the simulation.

Figure 3-3. Viewing the slabs to be sheared.

  1. Check the Show selected slabs in Workspace box
    • In the workspace, the slab will appear in a different color with nine large spheres, signifying the shearing plane/slab

Figure 3-4. Setting up the Thin Plane Shear calculation.

  1. Change the Job name to plane_shear_water09_glycerol91_20C
  2. Adjust the job settings () as needed
  3. Click Run
    • This job requires a CPU and GPU host. The job can be completed in about 30 minutes.
  4. If you would prefer to proceed with pre-generated results, you can import the results via File > Import Structures. Navigate to where you downloaded the tutorial files and choose Section_03 > plane_shear_water09_glycerol91_20C > plane_shear_water09_glycerol91_20C-out.cms
  5. Close the Thin Plane Shear panel
  6. Repeat this calculation for the other five remaining structures at their respective temperatures or proceed with the pre-generated results by importing in the five other output files

4. Analyzing Thin Plane Shear Calculations

In this section, we will analyze the thin plane shear calculation performed in Section 3 using the Thin Plane Shear Viewer panel.

Figure 4-1. Include and load the thin plane shear output.

All six results files have been imported into the project.

  1. With the water09_glycerol91_20C results entry 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 entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion, use the WAM button () to open the Thin Plane Shear Results panel
    • Alternatively, access the panel via Tasks > Materials > Classical Mechanics > Thin Plane Shear > Thin Plane Shear Viewer
    • The Thin Plane Shear Viewer panel opens

Figure 4-2. Thin plane shear summary results.

  1. If the results were not automatically loaded into the viewer click Load from Workspace
    • The Thin Plane Shear Viewer Panel shows the calculated viscosity and friction coefficient for the second half of the calculation
  2. Click the Shear Results tab

Figure 4-3. Thin plane shear graphed results.

This plot shows the drag force during the duration of the simulation. 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 good guess but it is not perfect. As the blue dashed vertical lines are adjusted, the viscosity and friction coefficients will adjust as well. The Y-Axis can also display the Friction Coefficient results.

 

  1. Click the Other Analysis tab

Figure 4-4. Thin plane shear graphed results.

  1. Close the Thin Plane Shear Viewer panel once finished

 

We see that the plot is more or less symmetric throughout the box height above and below a velocity of 0 Ang/ps. The plotted velocity is the average instantaneous velocity in the slab and therefore can be noisy.  

 

View the results of the five other systems using their WAM buttons. Below shows a graphical comparison of the results to see how temperature and concentration affects the velocity and number density.

The bulk system trajectory analysis for all six systems visualizes how velocity and number density changes throughout the system.

 

5. Conclusion and References

In this tutorial, we learned how to calculate the thin plane shear viscosity and friction coefficient for a water system using Materials Science (MS) Maestro.

For further learning:

For introductory content, focused on navigating the Schrödinger Materials Science interface, an Introduction to Materials Science Maestro tutorial is available. Please visit the materials science training website for access to 70+ tutorials. For scientific inquiries or technical troubleshooting, submit a ticket to our Technical Support Scientists at help@schrodinger.com.

For self-paced, asynchronous, online courses in Materials Science modeling, including access to Schrödinger software, please visit the Schrödinger Online Learning portal on our website.

For some related practice, proceed to explore other relevant tutorials:

For further reading:
  • Physical Properties of Aqueous Glycerol Solutions. Journal of Petroleum Science and Engineering 2012, 98–99, 50–60. DOI: 10.1016/j.petrol.2012.09.003.
  • Shearing friction behaviour of synthetic polymers compared to a functionalized polysaccharide on biomimetic surfaces: models for the prediction of performance of eco-designed formulations. DOI: 10.1039/D2CP05465E.
  • Reliable Viscosity Calculation from Equilibrium Molecular Dynamics Simulations: A Time Decomposition Method. DOI:10.1021/acs.jctc.5b00351
  • Best Practices for Computing Transport Properties 1. Self-Diffusivity and Viscosity from Equilibrium Molecular Dynamics. DOI:10.33011/livecoms.1.1.6324
  • Effects of Temperature Control Algorithms on Transport Properties and Kinetics in Molecular Dynamics Simulations. DOI:10.1021/ct400109a
  • Bird, Stewart and Lightfoot, Transport Phenomena, John Wiley & Sons, Inc., Revised Second Edition, 2007.

6. Glossary of Terms

Entry List - a simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion

Included - the entry is represented in the Workspace, the circle in the In column is blue

Project Table - displays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data

Recent actions - This is a list of your recent actions, which you can use to reopen a panel, displayed below the Browse row. (Right-click to delete.)

Scratch Project - a temporary project in which work is not saved, closing a scratch project removes all current work and begins a new scratch project

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

Working Directory - the location where files are saved

Workspace - the 3D display area in the center of the main window, where molecular structures are displayed