Penetrant Loading

Tutorial Created with Software Release: 2025-4
Topics: Consumer Packaged Goods, Pharmaceutical Formulations, Polymeric Materials
Methodology: All-Atom Molecular Dynamics
Products Used: Desmond, MS Maestro, MS Penetrant Loading

Tutorial files

0.2 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 learn to use the penetrant loading and viewer panels to place water molecules into a crosslinked polymer matrix using grand canonical Monte Carlo and molecular dynamics simulation.

 

Tutorial Content

  1. Introduction to Penetrant Loading

  1. Creating Projects and Importing Structures

  1. Loading the System with a Penetrant

  1. Analyzing the Penetrant Loading

  1. Conclusion and References

  1. Glossary of Terms

1. Introduction to Penetrant Loading

The Penetrant Loading and Viewer panels allow for the simulation of loading a condensed system (e.g. polymer, zeolite or molecular solid) with a small molecule (e.g. water, methane or hydrogen). In Schrödinger’s Materials Science (MS) Maestro suite, a periodic condensed system can be loaded with a penetrant following a straightforward workflow as summarized here:

The calculation effectively involves transferring penetrant molecules from a separate vapor phase into the condensed phase provided. When converged, the calculation provides a measure of the hygroscopicity or loading capacity of the condensed phase. The workflow proceeds via multiple cycles of a two-stage simulation process. First, grand canonical ensemble Monte Carlo (GCMC) simulations are used to place penetrants into vacancies in a condensed system. The Grand Canonical ensemble describes a system wherein chemical potential, volume and temperature are held constant. The chemical potential is held constant by coupling to an external bath of penetrant molecules, commonly called a reservoir. Insertion or deletion of particles is performed randomly based on Monte Carlo acceptance criteria. In the second stage, the system is relaxed using molecular dynamics (MD) simulation. These stages are performed iteratively for the simulation time. After the calculation, a viewer panel is utilized to analyze the percent weight penetrant, volume or number of penetrant molecules over time.

Penetrant Loading calculations are useful for a variety of applications. For examples, you can read more about penetrant loading in Polymeric Materials and Pharmaceutical Formulations on the Schrödinger website.

In this tutorial, we will load a provided crosslinked polymer system (already built and equilibrated as described in the Crosslinking Polymers tutorial) with water molecules using the Penetrant Loading calculations and viewer panels in MS Maestro.

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 created, the project is automatically saved each time a change is made.

Structures can be imported directly or from your Working Directorythe location where files are saved using File > Import Structures, 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/penetrant_loading.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 penetrant_loading_tutorial, click Save
    • The project is now named penetrant_loading_tutorial.prj

Figure 2-3. Importing the crosslinked polymer.

  1. Go to File > Import Structures
  2. Navigate to where you downloaded the tutorial files (presumably your working directory) and choose initial_configuration.cms from the provided files
  3. Click Open
    • A new entry group is added to the entry list containing an entry titled TGDDM33DS_DOS_amorphous

Note: This crosslinked polymer was prepared as detailed in the Crosslinking Polymers tutorial. For practice building crosslinked polymer systems, revisit that tutorial.

3. Loading the System with a Penetrant

In this section, we will use the Penetrant Loading panel to prepare and run the GCMC and MD simulations with water. The input system should be a well-relaxed MD output, as we have provided here.

Figure 3-1. Opening the Penetrant Loading panel.

  1. Ensure that TGDDM33DS_DOS_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 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 > Classical Mechanics > Penetrant Loading > Penetrant Loading Calculations

Figure 3-2. Preparing the Penetrant Loading panel and running the job.

  1. Change the Simulation time to 50 ns and the Trajectory recording interval to 25 ps
  2. Retain all other default settings in the panel (discussed in more detail below)
  3. Change the Job name to penetrant_loading_crosslink_water

 

Adjust the job settings () as needed. This job requires a GPU host. The job can be completed in about 1.5 hours

  1. If you would prefer not to run the job, import Section_03 > penetrant_loading_crosslink_water > penetrant_loading_crosslink_water-multisim-out.cms from the provided tutorial files. Otherwise, click Run
  2. Close the Penetrant Loading 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.

Let’s understand the settings and capabilities of the Penetrant Loading panel a bit more:

  • With respect to the penetrants:
    • The Penetrant can be retained as the default (SPC water), or you can Load a rigid penetrant other than water (implemented as no heavy atom torsions) from an entry in your project
    • The Vapor pressure is used to compute the system’s chemical potential (which will strongly influence the GCMC stage). You can set the vapor pressure manually, or, if loading water into the system, you can adjust the Relative humidity slider. If you load a penetrant other than water, you must choose a value for the Vapor pressure.
  • With respect to the simulation protocols:
    • The Simulation protocols section defines the conditions for the molecular dynamics stage of the penetrant loading process
    • The NPT Ensemble class will hold the pressure constant and allow the volume of the unit cell to change, which may be good for substrates that swell (as is the case for this crosslinked polymer example).
    • In cases where swelling is not expected (for example, a rigid zeolite), or in cases where an NPT class may result in indefinite expansion (for example, a system composed of small molecules), you can use the NVT ensemble to hold the volume constant. An anisotropic barostat can be used for systems that are expected to swell non-uniformly (for example, a semicrystalline polymer).
  • Visit the help documentation for a complete summary of the parameters

4. Analyzing the Penetrant Loading

In this section, we will visualize the output of the penetrant loading calculation both visually in the workspace and more quantitatively in the Penetrant Loading Viewer panel.

Figure 4-1. The output of the penetrant loading calculation.

When the job is complete or after importing, a new entry is added to the entry list entitled TGDDM33DS_DOS_amorphous:

  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 entry

 

Note: If your output is not contained inside the unit cell, this is purely visual, but you can use the Periodic Structure Tool Window () to Build Cell > Translate to First Unit Cell > Apply (click Continue if a warning appears) and the atoms will all be translated into a single unit cell.

Figure 4-2. Selecting just the water molecules.

We can change the style of just the water molecules so that they are easier to visualize in the cell.

  1. From the Toolbar, use the Quick Select dropdown and choose Waters
    • All of the water molecules are 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 workspacethe 3D display area in the center of the main window, where molecular structures are displayed

Figure 4-3. Changing the style of the water molecules.

  1. From the Toolbar, click on the Style palette () and choose Apply CPK Representation
    • All of the water molecules are now shown with CPK representation in the workspace

 

Note: If you wish to change the style of the polymer as well, the most convenient way to 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 the atoms associated with the polymer is to again select the water molecules and then use the Invert button in the toolbar to switch the selection to everything but the water molecules.

Figure 4-4. The halfway point of the trajectory (water molecules have been stylized again).

Note that the current model in the workspace is the last frame after the 50.0 ns MD simulation. If you are interested in viewing the entire simulation to visualize the penetration of water over time, feel free to open the trajectory viewer ().

 

If you are unfamiliar with using the Trajectory Viewer, revisit Section 5 of the Building, Equilibrating and Analyzing Amorphous Polymers tutorial.

Figure 4-5. Opening the Results panel.

Now we will open the Penetrant Loading results panel to extract some quantitative metrics from our simulation. Despite the fact that only the last frame is shown in the workspace, this panel provides analysis over the entire course of the trajectory.

  1. Use the WAM () button to access the Penetrant Loading Viewer panel
    • Alternatively, go to Tasks > Materials > Classical Mechanics > Penetrant Loading > Penetrant Loading Results and click Load Data from Workspace

Figure 4-6. Viewing the % Weight Penetrant versus Time.

The first plot provided is the % Weight Penetrant versus Time (ns) for the simulation.

The green slider can be adjusted as needed to determine the plateau value for the property of interest (the Slider value box will update interactively).

The Average properties section displays the average value of the active property. You can adjust the time range over which this average is taken.

  1. Change the Time range to start at 15 ns

Note: In this instance, the simulation reaches a clear plateau after approximately 15 ns and only fluctuates around a mean value.

Figure 4-7. Viewing the Volume change over time as well.

Let’s also analyze how the volume of the system changes with time. Recall that we ran an NPT simulation and we expect swelling to occur.

  1. Check Add second property and retain Volume from the dropdown
    • The plot is updated to include a second property, volume
    • Note that the slider now refers to the volume data, though the average properties includes readouts for both properties
    • Move the legend by clicking and dragging as needed

 

Feel free to explore the Viewer panel further. In addition to % Weight Penetrant and Volume, you can also analyze the Number of Penetrant molecules over time.

5. Conclusion and References

In this tutorial, we learned how to use the penetrant loading and viewer panels to place water molecules into a crosslinked polymer matrix.

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:

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