Thermal Conductivity

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

Tutorial files

53 MB
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 learn to use the Thermal Conductivity Calculation and Results panels to calculate the thermal conductivity of two systems: ethanol and amorphous polyamide-6,6.

 

Tutorial Content

  1. Introduction to Thermal Conductivity

  1. Creating Projects and Importing Structures

  1. Thermal Conductivity of Ethanol

  1. Thermal Conductivity of Polyamide-6,6

  1. Conclusion and References

  1. Glossary of Terms

1. Introduction to Thermal Conductivity

Simulation based design of novel materials offers significant acceleration to the materials discovery cycle. Molecular Dynamics (MD) is a powerful tool that provides a deep understanding of materials’ behavior and aids in the design and optimization process. It helps capture the dynamics of the materials at a very small time and length scale that is often unattainable by experimental methods. Thermal conductivity is a material property that describes the ability of a substance to conduct heat. It is a measure of the ease with which heat can flow through the substance in the presence of a temperature gradient. The relationship between heat transfer and the temperature is given by Fourier’s law of heat conduction:

Here, is the heat flux, k the thermal conductivity, and the temperature gradient.

The RNEMD (Reverse Non-Equilibrium Molecular Dynamics) method is a computational technique used to calculate thermal conductivity in materials. In this method, the simulation box is divided into small slabs in one direction and a heat flux is induced through the material by exchanging the velocity of the “hottest” atom in the cold slab and the “coldest” atom in the hot slab. The heat flux (q) between the hot and the cold slab is given by:


Here, the sum is taken over all exchange events through the simulation time t. and correspond to the velocity of the hot and the cold atoms respectively of mass and . The terms in the denominator and refer to the box dimension of the plane perpendicular to the flux direction (). The thermal conductivity can be calculated by measuring the resulting temperature gradient in the z-direction. (See References):

In simulations, finite size effects can lead to inaccuracies. The quantization of vibrational energy levels (phonons) can be a source of error in the calculation of the thermal conductivity below the Debye temperature (θD). Therefore corrections need to be applied to account for phonon scattering that can affect the heat transfer (see References). The thermal conductivity calculated using the RNEMD method can be corrected for the error using a quantum correction:

Here, can be obtained from the vibrational density of states. For more information please refer to the help documentation.

In this tutorial, we will calculate and analyze the thermal conductivity of ethanol and polyamide-6,6 (nylon-6,6) using the Thermal Conductivity Calculation and Thermal Conductivity Results panels. The overall workflow is as depicted below:

For a related workflow on predicting the glass transition temperature (Tg), see the Polymer Property Prediction and the Glass Transition Temperature for Active Pharmaceutical Ingredients (API) tutorials.

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: https://www.schrodinger.com/sites/default/files/s3/release/current/Tutorials/zip/thermal_conductivity.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 thermal_conductivity_tutorial, click Save
    • The project is now named thermal_conductivity_tutorial.prj

Figure 2-3. Imported structures in the entry list (ethanol is included in the workspace).

The starting structures for both systems are provided: ethanol and an equilibrated cell of amorphous polyamide-6,6:

  1. Go to File > Import Structures
  2. Navigate to where you downloaded the tutorial files (presumably in your working directory), and select ethanol.mae and disordered_system_polyamide_6-6_all_components_amorphous-out.cms. Click Open

3. Thermal Conductivity of Ethanol

In this section, we will use the Disordered System Builder to build a disordered simulation cell of ethanol and then calculate the thermal conductivity using the Thermal Conductivity Calculation panel.

Figure 3-1. Opening the Disorder 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 and includethe entry is represented in the Workspace, the circle in the In column is blue the ethanol entry from the group in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.
  2. Go to Tasks > Materials > Structure Builders > Disordered System

 

Note: For general practice with the Disordered System Builder, see the Disordered System Building and Molecular Dynamics Multistage Workflows tutorial

Figure 3-2. Setting up the Components tab.

We will generate an amorphous cell of ethanol in a box with dimensions a = b ≤ c/2~c/4. These approximate dimensions are necessary to generate bins of sufficient width (~10 angstrom) in the z-direction for the subsequent thermal conductivity calculation.

  1. Change Initial state to Amorphous
  2. For Number of molecules input 2000
  3. Go to the Disorder tab

Figure 3-3. Setting up the initial density.

  1. Change Initial density to 0.7
    • The experimental density of ethanol is 0.78 g/mL so the initial density of the system is increased from the default value.
  2. Go back to the Components tab in the Disordered System Builder panel

 

Figure 3-4. Running the Disordered System Builder.

  1. Check Custom PBC dimensions (Å) and input 47.0 for both a and b vectors
    • The dimension for c vector is automatically updated to 98.9 Å
    • In this case a = b ≈ c/2
  2. Change the Job name to disordered_system_ethanol
  3. This job takes ~5 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 structure, you can import the amorphous cell via File > Import Structures. Navigate to where you downloaded the tutorial files and choose the Section_03 > disordered_system_ethanol > disordered_system_ethanol-out.cms file.

  1. Close the Disordered System Builder panel

Figure 3-5. Opening the Thermal Conductivity Panel.

When the job is finished or after importing, feel free to stylize and visualize the output.

  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 disordered_system_ethanol_all_components_amorphous entry in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.
  2. Go to Tasks > Materials > Thermal Conductivity > Thermal Conductivity Calculations

Figure 3-6. Setting up and running thermal conductivity calculation.

  1. Ensure that the Add relaxation step is checked
    • The panel has an option to add a pre-relaxation step prior to the thermal conductivity calculation. For small organic molecules, this relaxation is sufficient to proceed with the calculation. We will see in Section 4 that for polymers we need to equilibrate using the MD Multistage Workflow panel before running the calculation. For details about the relaxation protocol, please visit the help documentation.
  2. Change the Temperature gradient direction to c
  3. Check Set random number seed
  4. Check Correction for frozen phonons
  5. Change the Job name to thermal_conductivity_ethanol
  6. Adjust the job settings () as needed
    • This job requires a GPU host. The job can be completed in about 2 hours
  7. If you would like to run the job, click Run. Otherwise, pre-generated results are provided.

If you would prefer to proceed with pre-generated structure, you can import the amorphous cell via File > Import Structures. Navigate to where you downloaded the tutorial files and choose the Section_03 > thermal_conductivity_ethanol > thermal_conductivity_ethanol-out.cms file.

Figure 3-7. Opening the Thermal Conductivity Results panel using the WAM.

To view the results of the thermal conductivity calculation, we use the Thermal Conductivity Results panel:

  1. When the job is finished or after importing, use the WAM (Workflow Action Menu) button() to open the Thermal Conductivity Results panel
    • Alternatively access the panel via Tasks > Materials > Thermal Conductivity > Thermal Conductivity Results
    • The Thermal Conductivity Results panel opens

Figure 3-8. Thermal Conductivity Results panel.

The Summary tab shows a comprehensive summary of the calculation including information about the system, the bin size, etc. The thermal conductivity of ethanol is calculated to be ~226 milli-W/mK. With quantum correction, the value is ~116 milli-W/mK.

 

The values predicted from the panel are ~±30% from the experimental value for ethanol at 300 K (171 milli-W/mK).

 

  1. Go to the Temperature Gradient tab.

Figure 3-9. Viewing the temperature gradient in the Thermal Conductivity Results panel.

This tab includes a plot showing the temperature gradient in the system. In this case, the gradient is linear. The range of values from which the gradient, and thereby the thermal conductivity, is calculated can be adjusted by moving the edges of the blue and the green regions. The temperature gradient is 0.5 K/Å.

 

  1. Go to the Convergence tab.

Figure 3-10. Convergence of thermal conductivity.

The thermal conductivity converges to a stable value after ~10 ns.

  1. Close the Thermal Conductivity Viewer panel

4. Thermal Conductivity of Polyamide-6,6

In this section, we will use a pre-equilibrated simulation cell of amorphous polyamide-6,6 and follow a similar protocol used in the previous sections to calculate the thermal conductivity.

Figure 4-1. Selecting the polyamide-6,6 structure.

  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 disordered_system_polyamide_6-6_all_components_amorphous entry in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.

Before proceeding to the thermal conductivity calculations, we will look at the procedure for building and equilibrating the amorphous polymer system.

 

In this case, we build an amorphous cell of 48 chains of polyamide-6,6 polymer with 20 repeat units in a box with dimensions 70.0 70.0147.3 Å3 using the Disordered System Builder Panel. This cell is then subjected to the Bulk macromolecule relaxation protocol in the MD Multistage Workflow Panel which consists of:

  1. Brownian minimization stage
  2. 24 ps NVT MD stage at 300 K
  3. 240 ps NVT MD stage at 700 K
  4. 24 ps and 240 ps NPT MD stages at 300 K and 1.01345 bar
  5. 10000 ps NPT simulated annealing stage at 1.01325 bar
  6. 10000 ps NPT MD stages at 300 K and 1013.25 bar
  7. 10000 ps NPT MD stages at 300 K and 1.0125 bar

 

Following the relaxation protocol, the density of the system was calculated to be 1.071 g/cm3 which is similar to the value of 1.07g/cm3 reported by Lussetti et al. (See References). We will use this equilibrated structure for the thermal conductivity calculations.

Figure 4-2. Opening the Thermal Conductivity Calculation panel.

  1. Go to Tasks > Materials > Thermal Conductivity > Thermal Conductivity Calculations

Figure 4-3. Setting up and running the Thermal Conductivity Calculation panel.

  1. Uncheck the Add relaxation step
    • Since the system is already equilibrated a relaxation step does not need to be added
  2. Change the Temperature gradient direction to c
  3. Check Correction for frozen phonons
  4. Change the Job name to thermal_conductivity_polyamide_6-6
  5. Adjust the job settings () as needed
    • This job requires a GPU host. The job can be completed in about 3.5 hours
    • If you would like to run the job, click Run. Otherwise, pre-generated results are provided

If you would prefer to proceed with pre-generated structure, you can import the amorphous cell via File > Import Structures. Navigate to where you downloaded the tutorial files and choose the Section_04 > thermal_conductivity_polyamide_6-6 > thermal_conductivity_polyamide_6-6-out.cms file.

Figure 4-4. Opening the Thermal Conductivity Results panel using the WAM button.

  1. When the job is finished or after importing, use the WAM button() to open the Thermal Conductivity Results panel
    • Alternatively access the panel via Tasks > Materials > Thermal Conductivity > Thermal Conductivity Results

Figure 4-5. Thermal Conductivity Results panel.

The thermal conductivity of amorphous polyamide-6,6 is calculated to be ~297 milliW/mK. With quantum correction, the value is ~200milliW/mK. This value is within the experimental range of 150-300 milli-W/mK reported in literature (See Lussetti et al).

 

Feel free to explore the results panel further.

5. Conclusion and References

In this tutorial, we learned how to calculate the thermal conductivity of a small organic molecule and an amorphous polymeric system.

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 100+ 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:

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