Building, Equilibrating and Analyzing Amorphous Polymers

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

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

 

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Abstract:

 

In this tutorial, we will learn the basics of building an amorphous cell of polymers, equilibrating the cell using molecular dynamics and analyzing the equilibrated cell.

 

Tutorial Content

  1. Introduction to Building Polymers

  1. Creating Projects and Importing Structures

  1. Building a Homopolymer Amorphous Cell

  1. Generating a Co-Polymer Chain and Building an Amorphous Cell

  1. Running a Molecular Dynamics Simulation

  1. Calculating Density and Solubility Parameters 

  1. Polymer Chain Analysis

  1. Conclusion and References

  1. Glossary of Terms

1. Introduction to Building Polymers    

Polymers are a critical class of materials central to applications from advanced carbon-fiber composites and structural organics, to semiconductor and electronics manufacture and packaging. Development of next generation polymer systems can be enabled by Schrödinger’s Materials Science Suite capabilities for in silico design and analysis of various polymer chemistries. This tutorial will help you become familiar with the basics of polymer modeling.

A polymer is a material which consists of repeating subunits (monomers) that have joined together in a polymerization process. Polymers can be classified based on their overall structure.  There are four main categories of polymer structures - linear, branched, dendritic and networked. Within each category, structural characteristics of the polymers can vary. For example, linear polymers may be homopolymers or copolymers, and copolymers themselves may be of highly ordered or random composition. Networked polymers are discussed in the Crosslinking Polymers tutorial.

For simulation, a molecular model must be constructed based on the atomic composition of the material. In the case of polymers, generation of starting models can be tedious via traditional drawing or building methodologies. In Materials Science (MS) Maestro, the Polymer Builder allows for facile construction of various initial polymer structures based on minimal inputs (monomer types, connection points, chain lengths, etc.). Construction of linear, branched and dendritic polymers of any complexity is possible.

A polymer can be constructed using the Polymer Builder by simply selecting or sketching a monomer, defining its head and tail and using this repeat unit to build the repeating chain. After building a polymer chain, we can use the chain as a single component in an amorphous cell or as one of several components in a more complex solution. With polymer modeling, typically we will be constructing amorphous cells, which are periodic unit cells packed with polymer chains.

It is important to note that the outputs from the polymer builder themselves are not accurate representations of the bulk material. After building the initial cell, we must use molecular dynamics (MD) to equilibrate the structure. Indeed, the resultant cell can then be used for predicting bulk properties or as an input for simulations towards determining other mechanical properties like glass transition and elastic response (see the Polymer Property Prediction tutorial).

In this tutorial, we will learn a typical workflow for preparing simple polymer models. We will generate two amorphous cells: first, an amorphous cell built from a polyethylene homopolymer, and then an amorphous cell built from a single styrene-butadiene copolymer chain. We will equilibrate the polyethylene amorphous cell with an MD simulation and then analyze several metrics associated with the polymer chain structures using the Polymer Chain Analysis tools.

Here is a schematic of the overall general workflow:

After completing this tutorial, if you are interested in other types of polymeric structures, please visit the tutorials listed in Section 8 for further learning.

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/builders_polymer.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
    • The titles of the subdirectories within the zip file correspond to the different sections of this tutorial

Figure 2-2. Save Project.

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

3. Building a Homopolymer Amorphous Cell

In this section, we will use the Polymer Builder to generate a cubic amorphous cell of multiple polymer chains starting from an ethylene monomer. Amorphous cells can also be generated using the Disordered System Builder, for more see the Disordered System Building and Molecular Dynamics Multistage Workflows tutorial. We will use this structure as a starting point for a molecular dynamics simulation in Section 5. Sections 6 and 7 will go through common analyses to learn more about the structural features of our polyethylene polymer cell. To learn more about building amorphous polymers watch Getting Going with Materials Science Maestro Video Series: Building Amorphous Polymers.

Figure 3-1. Opening the Polymer Builder.

  1. Go to Tasks > Materials > Structure Builders > Polymer

 

Note: We will frequently use the Polymer Builder panel in this tutorial. To make it easier to find the panel, you can click the star next to the panel name in the task menu and it will be added as a favorite to your toolbar

Before building our polymers of interest, let’s take a moment to understand in detail the Polymer Builder Panel:

  • The panel consists of four tabs in which selections are made to inform the polymer build:
  • In the Groups tab you can specify the chemical groups you want to use for the polymer build
    • For Monomer type, there are three options; all-atom, coarse-grained, and carbohydrate. In this tutorial we will use all-atom monomers, but for examples of polymer builds consisting of other monomer types, please see Building a Coarse-Grained Polymer Model and Building a Carbohydrate Polymer
    • For a given Monomer type you can specify the initiator, cascader, terminator, and monomers, by using built-in options or by sketching the structure. Cascaders are used for generating dendritic structures.
    • Monomers can be added or deleted using the Add Monomer and Delete buttons. The monomers are labeled with letters, A, B, C, and so on. These letter codes are used in the Composition tab to specify the order in which the monomer units are used
  • In the Composition tab you can specify how the monomers are arranged to form the polymer, and the number of repeat units in the polymer. The type of polymer that can be formed depends on the number of monomer units, and is reflected in the options of this section
  • In the Chain Growth tab you can specify parameters for the growth of the polymer chain, such as Nonstandard coupling probabilities and Backbone dihedrals
  • In the Amorphous Cell tab you can create one or more cubic amorphous cells from each of the polymers that you build. The size of the cell is determined from the number of polymer molecules and the final density. The periodic boundary condition properties are added to the structure when the cell is created
    • Create amorphous cell must be checked in order to define the rest of the parameters in this section
    • Many of the parameters in this section set how the amorphous cell will be packed with polymer units. For more background on how the cell is formed, please see the help documentation
    • Number of polymers specifies the number of polymer chains to place in the cell
    • The Initial density and Initial clash VDW scale factors are set to reasonable defaults, as discussed in detail later in this Section. One is kept constant and the other will be adjusted to avoid clashes as the cell is packed with polymers
    • The Create system for Desmond calculations ensures that the model system can be input for molecular dynamics simulations with Desmond. If you intend on running a molecular dynamics workflow on the amorphous cell, this option should be selected

For a more comprehensive overview, see the help documentation on the panel.

 

Note: The monomer structure, end groups, tacticity, and composition for polymers are frequently available from polymer handbooks, vendor data sheets, or experimentation. That information should be collected prior to building the amorphous polymer structure. In this tutorial, we will provide the information needed to build our two polymer cells.

Figure 3-2. Choose the Initiator and Terminator.

To generate our polyethylene amorphous cell, we must first specify the end groups of a polymer chain

  1. For Initiator, choose H
  2. For Terminator, choose H

Hydrogen should be the default end group, however you can choose other common groups in the option menu. If a group that you need is not on the menu, it is possible to sketch and name a custom end group for use

Figure 3-3. Defining a monomer.

Next, we will define the monomer that makes up our polymer chain, ethylene. We will add ethylene from the predefined monomer library

  1. Under Monomers, next to A, from Custom choose ethylene

In the Polymer Builder panel monomers are shown as the repeat unit after polymerization, with head and tail labeled. Hover over the chemical formula shown next to ethylene to see a sketch of the structure and its designated head and tail. The groups that designate the head and tail of a monomer unit, are denoted as R1 and R2 respectively.

Figure 3-4. Setting the polymer composition.

  1. Click the Composition tab
  2. Under Homopolymer set the Number of monomers to 20
    • The length of a single homopolymer chain will consist of 20 ethylene monomer units
    • The bottom of the panel updates and the new total atoms per chain and molecular weight are shown

Figure 3-5. Generating an amorphous cell.

  1. Click the Amorphous Cell tab
  2. Check Create amorphous cell
  3. Check Entangled chain growth
  4. For Dihedral angle distribution select Uniform
  5. For Number of polymers, enter 100
    • 100 polymers chains will make up the cubic amorphous cell
    • Each chain will consist of 20 monomers, as defined above
  6. Ensure that Create system for Desmond calculations is checked

 

Note: Here we leave the Initial density set as the default, 0.5 g/cm3. In general, it is advised in the building stages to pack the cell to lower density than the expected density. The default of 0.5 is a good choice in most instances. During the MD simulation(s), the box will densify. If during the building stage we attempt to pack the cell to the expected density, the job may either take a long time or crash altogether

 

Note: Polydisperse homopolymers can be built once Create amorphous cell has been checked off. In the Composition tab, a new feature has been enabled, a Flory-Schulz distribution of polymer lengths instead of a fixed length. Please see the Polydispersity Reference Sheet for how to use this feature.

Figure 3-6. Running the polymer builder.

  1. Change the Job name to polyethylene_cell
  2. Adjust the job settings () as needed
    • This job requires a CPU host. The job can be completed in less than 5 minutes on a CPU host
  3. If you would like to run the job, click Run. Otherwise, we will proceed with pre-generated results in the next step
  4. Once the job is successfully completed, a new polyethylene_cell_system group, with a single entry titled amorphous poly(ethylene), 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 in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and is includedthe entry is represented in the Workspace, the circle in the In column is blue in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
  5. Close the Polymer Builder panel

Figure 3-7. Viewing the amorphous cell in the workspace with the unit cell.

  1. Go to File > Import Structures, navigate to the provided tutorial files and Open Section_03 > polyethylene_cell > polyethylene_cell_system-out.cms
    • 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
  2. 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 amorphous poly(ethylene)
  3. Open the Workspace Configuration Toolbar (clicking the icon in the bottom right corner of the workspacethe 3D display area in the center of the main window, where molecular structures are displayed)
  4. Ensure that Unit Cell is toggled on
    • Unit Cell view is displayed in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
  5. Close the Workspace Configuration Toolbar (clicking the icon in the bottom right corner of the workspacethe 3D display area in the center of the main window, where molecular structures are displayed)

 

Note: If you ran the calculation, the polyethylene cell built may not be an exact replica of the provided cell due to random dihedrals angles and the view angle

Figure 3-8. Viewing the copolymer amorphous cell. 

The amorphous cell in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed

We will come back to this amorphous cell in Section 5 and run a molecular dynamics simulation

4. Generating a Co-Polymer Chain and Building an Amorphous Cell

Let’s look at a slightly more complex example, in which we will use the Polymer Builder to generate a single styrene-butadiene copolymer chain. The single copolymer chain can be used as a single component in an amorphous cell or as one of several components in a more complex solution. In this tutorial, we will use the styrene-butadiene copolymer chain and the Polymer Builder to build a cubic amorphous cell. The Disordered System Builder can also be used to create periodic cells. The Polymer Builder used here will only take one polymer chain as input, which is why it is sufficient in our example. On the other hand, the Disordered System Builder can take many polymers as inputs and create a unit cell of them, making it especially useful for more complex solutions. For examples of multi-component builds using the Disordered System Builder, please visit the following tutorials: Disordered System Building and MD Multistage Workflows, Viscosity, Calculating Surfactant Tilt of a Bilayer System, and Building a Polymer-Polymer Interface Model. We will not run any further calculations on the final amorphous cell in this section. If you are interested, feel free to use Sections 5, 6, and 7 as guidance for subsequent analysis of the styrene-butadiene amorphous cell.

Figure 4-1. Opening the Polymer Builder from favorites.

  1. Go to your favorites bar and click on Polymer Builder
    • Alternatively, go to Tasks > Materials > Structure Builders > Polymer
    • The Polymer Builder opens

Figure 4-2. Selecting end groups.

To generate our styrene-butadiene copolymer, we must first specify the end groups of the single polymer chain

  1. For Initiator, choose H
  2. For Terminator, choose H

Figure 4-3. Defining the monomers.

Next, we will define the monomers that make up our copolymer chain, styrene and butadiene. Similar to end groups, you can choose a monomer from the option menu or draw a custom monomer. We will add styrene from the predefined monomer library

  1. Under Monomers, next to A, from Custom choose styrene
  2. For Tacticity, choose Atactic

Figure 4-4. Adding a monomer.

Butadiene will be built using the Monomer Sketcher

  1. Click Add Monomer
    • Monomer B is added
  2. Next to B, click Sketch
    • The Monomer Sketcher opens

Figure 4-5. Sketching a monomer.

  1. Draw the molecule shown in the Figure
    • The carbon atoms, left to right, are referred to as C1, C2, C3, C4, C5, and C6

Note: The Monomer sketcher functions like many standard 2D molecular drawing tools. For a complete overview of using the sketcher panel, see the 2D Sketcher Panel documentation

 

Note: A 3D structure can also be used by clicking Import from Workspace

Figure 4-6. Defining R1.

R-groups are used to define the linkage points for the monomers to join together to form the polymer chain. The R-group will be discarded when forming a bond with the subsequent incoming monomer. Denoted as R1 and R2, the groups designate the head and tail of a monomer unit, respectively.

  1. Right-click on C1 (designated by just the end-point of the line on the left) as shown in the Figure
  2. Choose Replace with > New R-Group

Note: If you want to create branched polymers, you can add an R3 group to the monomer to designate a point where a new chain can be attached. In this tutorial, we will only be making linear homopolymers

Figure 4-7. Defining R2.

  1. Repeat Steps 9-10 for C6 (designated by just the end-point of the line on the right) and set as R2
    • R1 and R2 designate the head and tail of the monomer unit

Figure 4-8. Finalizing the butadiene monomer.

The structure in the Monomer Sketcher should match that which is shown in the Figure

  1. Click Use This Structure
    • The sketcher closes and Custom appears for Monomer B

Figure 4-9. Naming the monomer.

  1. Next to Name for monomer B, type butadiene

Figure 4-10. Specifying the composition of the polymer.

  1. Click the Composition tab
  2. Choose Random copolymer
    • We will generate a copolymer chain where the monomer units will be polymerized in a random order

Figure 4-11. Setting the propagation definition preference and data.

To better specify distribution of monomers along the polymer chain, we will use the Propagation definition preference options. By selecting this, we can provide propagation data, such as Coupling probability or Reactivity ratio in the data table. Coupling is always tail-head when propagation is specified. Each row or column corresponds to a particular monomer and each ij entry is the j monomer extending an i chain end. If you choose Reactivity ratio, the diagonal values cannot be set, as they are by definition 1.

  1. Check Propagation definition preference:
    • This setting must be selected before entering Monomer concentration
  2. Select Reactivity ratio
  3. In the matrix, A-B cell, type 1.70
  4. In the matrix, B-A cell, type 0.7
    • The reactivity ratios are a ratio of k12/k11 in a polymer addition growth reaction

Note: The reactivity ratios used to build our styrene-butadiene copolymer were adapted from Seo KS, et al. (2018) Determination of Reactivity Ratios for α-Methylstyrene- Butadiene Copolymerization via Cesium-based Catalyst System. In practice, reactivity ratios depend on the catalyst and production system used.

Figure 4-12. Specifying monomer concentrations.

  1. For Monomer concentration, set A to 20 and set B to 80
    • The relative composition of the monomers is 20% styrene and 80% butadiene
  2. For Number of Monomers, type 15
    • Approximate composition is set to A4 B11, which corresponds to approximately 4 monomers of styrene and 11 monomers of butadiene in the copolymer chain

Note: The reactivity ratio set in previous steps impacts the composition of the polymer chain on top of the monomer concentration. The approximate composition of a 15 monomer chain is A4 B11 which is not exactly equivalent to the relative composition of 20% styrene and 80% butadiene. If each row and column in the reactivity ratio matrix remained the default value of 1, then the approximate composition would equal the relative composition.

Figure 4-13. Specifying chain growth.

  1. Click the Chain Growth tab
  2. For Backbone dihedral, choose Random
    • Selecting random here is a reasonable way to generate a good starting point for eventually calculating an accurate model. Without random dihedral angles, the chain will be built as a rigid straight line
  3. For Affected dihedrals, choose All

Figure 4-14. Running the polymer builder.

If we run the job now before proceeding to the Amorphous Cell tab, we will build a single non-periodic chain of the copolymer. Let’s do so, then we will return to the panel to build a cell

  1. Change the Job name to styrene_butadiene_chain
  2. Adjust the job settings () as needed
    • This job requires a CPU host. The job can be completed in less than one minute on one processor
  3. Click Run
  4. Once the job is successfully completed, a new styrene_butadiene_chain_polymer1 group, with a single entry titled poly(styrene/butadiene), 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 in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and is includedthe entry is represented in the Workspace, the circle in the In column is blue in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed

Figure 4-15. Viewing the copolymer colored by monomer type.

The random copolymer can be visualized in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed. The single copolymer chain can be used in a variety of polymer builds as described above. Now, we will make a cubic amorphous cell using multiple copolymer chains.

As shown in the Figure, the random copolymer was colored by monomers, the different carbon atoms were given 2 different colors, and stylized as ball-and-stick using the Style icon. Feel free to stylize as you wish.

Figure 4-16. Specifying the amorphous cell.

  1. Returning to the Polymer Builder panel, click the Amorphous Cell tab
  2. Check Create amorphous cell
  3. Check Entangled chain growth
  4. For Dihedral angle distribution select Boltzman
  5. For Number of polymers, enter 85
    • 85 copolymers chains will make up the cubic amorphous cell
  6. Ensure the rest of the options in the Amorphous Cell tab match those shown in the Figure

Figure 4-17. Running the polymer builder.

  1. Change the Job name to styrene_butadiene_cell
  2. Adjust the job settings () as needed
    • This job requires a CPU host. The job can be completed in less than 45 minutes
  3. If you would like to run the job, click Run. Otherwise, pre-generated results are provided to view the structure
  4. Once the job is successfully completed, a new styrene_butadiene_cell_system group, with a single entry titled amorphous poly(styrene/butadiene), 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 in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and is includedthe entry is represented in the Workspace, the circle in the In column is blue in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
  5. Close the Polymer Builder panel

Figure 4-18. Viewing the copolymer amorphous cell.

  1. Go to File > Import Structures, navigate to the provided tutorial files and Open Section_04 > styrene_butadiene_cell > styrene_butadiene_cell_system-out.cms
  2. 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 amorphous poly(styrene/butadiene)

The amorphous cell can be visualized in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed. Feel free to examine this structure and perform further calculations if interested

Sometimes we need to build polymers that are obtained via a condensation reaction, where two types of monomers (e.g. A and B) can only react to form alternating -ABAB- type chains. If only one type of monomer A and monomer B are mixed, the case can be handled by the Periodic Copolymer option. However, if multiple types of monomer A and/or monomer B are used, the Random Copolymer option with defined coupling probability should be used. Let’s see an example with a polyurethane reaction, where one diisocyanate monomer (type A) is reacted with two different diols (type B1 and type B2).

From the molar ratio of the monomers, one can calculate the coupling probabilities to include in the panel. All undesired coupling should be set to zero (e.g. A-A, B-B), while the other probabilities can be calculated by the fraction of the monomer over the total for that specific monomer type (e.g. for monomer type B1 the coupling probability is given by moles of B1 / (moles B1 + moles B2). For the example above, with a molar ratio of 3:2:1 for A:B1:B2, the coupling probabilities for the polymer builder panel would be the following:

5. Running a Molecular Dynamics Simulation

In this section, we will relax and equilibrate the amorphous polyethylene polymer cell built in Section 3. Our cell has 12,200 atoms which is a reasonable cell size for a simple amorphous homopolymer (10,000-20,000 atoms is a standard range for basic models). We use molecular dynamics (MD) to equilibrate the polyethylene structure in order to predict bulk properties from the resulting cell. We will run an analysis calculation as the last step of the workflow in this section. The properties calculated will be discussed in Section 6.

Figure 5-1. Using the WAM to open the MD Multistage Workflow.

The most convenient method to access the MD Multistage Workflow panel is by using the Workflow Action Menu (WAM) button which appears next to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion

  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 the polyethylene_cell_system entry group from Section 3, click on the WAM button and select MD Multistage Workflow
    • The MD Multistage Workflow panel opens
    • Alternatively, go to Tasks > Materials > Classical Mechanics > MD Simulations > MD Multistage Workflow

Let’s familiarize ourselves with how the MD Multistage Workflow panel is operated and navigated.

  • You can choose to run a relaxation protocol before starting the simulation. The built-in protocols that apply to your model system will be displayed in the option menu. You can also create and manage your own protocol
  • A stage is the type of calculation that will be run as a component of the workflow:
    • The stages available are Brownian Minimization, Molecular Dynamics, DPD Molecular Dynamics, Simulated Annealing, Average Cell, Deform Cell, and Analysis
  • Once you select a stage, various parameters can be defined for that stage. For example, for a Brownian Minimization, the following options are available:
  • Stages can be minimized, moved, duplicated and deleted using the stage management buttons:
  • Stages and workflows can be managed at the bottom of the panel:
    • To add a new stage, click Append Stage
    • You can Append Stages from File if you saved a workflow from a previous project or collaborator

Note: An Analysis stage will perform an analysis of the structure produced in the step directly before it.

For a more comprehensive overview, see the help documentation on the panel or the Disordered System Building and Molecular Dynamics Multistage Workflows tutorial.

 

 

Here we will use a relatively straightforward simulation protocol to equilibrate the system. First, the Materials relaxation protocol will be applied, which is a three step, simple workflow that is relatively robust. It includes a 20 ps NVT Brownian minimization at 10K, a 20 ps NPT Brownian minimization at 100K and a 100 ps NPT MD stage at 300K. This should help to densify the system before the molecular dynamics stage. Then we will implement a molecular dynamics stage to equilibrate the cell and gather trajectory data for analysis in the subsequent sections. Finally, we will perform bulk analysis on the system for a variety of standard properties. Note that protocols for MD simulations always depend on the system at hand as well as computational resources available.

Figure 5-2. Setting up the MD workflow.

  1. Check Relaxation protocol and select Materials relaxation
  2. In Stage 4, for Stage Type, choose Molecular Dynamics
  3. For Simulation time (ns), set total to 10
  4. For Recording interval (ps), set trajectory to 100 and energy to 5
  5. For Ensemble class, ensure NPT is selected
  6. Set the Temperature to 400
  7. Ensure that the MD Multistage Workflow panel is set as shown in the Figure

Figure 5-3. Adding a stage.

  1. Click Append Stage
    • Stage 5 is added to the workflow

Figure 5-4. Setting an analysis stage.

  1. In Stage 5, for Stage Type, choose Analysis

Figure 5-5. Running the MD workflow.

  1. For Job name, enter MD_polyethylene
  2. Adjust the job settings () as needed
    • This job requires a GPU host. The job can be completed in 2 hours
  3. If you would like to run the job, click Run. Otherwise, pre-generated results are provided to view the structure
  4. Once the job is successfully completed, a new MD: polyethylene_cell_system (1) group, with a single entry titled amorphous poly(ethylene), 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 in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and is includedthe entry is represented in the Workspace, the circle in the In column is blue in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
  5. Close the MD Multistage Workflow panel

Figure 5-6. Loading the trajectory.

  1. Go to File > Import Structures, navigate to the provided tutorial files and Open Section_05 > MD_polyethylene > MD_polyethylene-out.cms
    • 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
  2. 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 amorphous poly(ethylene)
  3. Click on the T button () next to this entry and select Load Trajectory
    • The trajectory is now loaded into the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed

Figure 5-7. Viewing the trajectory.

Each frame in a trajectory is a snapshot of the system at a specific time period (as designated in the MD parameters by the simulation time and recording interval). The Trajectory Player enables us to examine individual frames or play the frames sequentially to visualize the course of the MD simulation. Subsequent analysis can be performed on single frames, the entire trajectory or portions of the trajectory depending on the project goals. In general, analysis data should be extracted from equilibrated trajectories, so occasionally only latter segments should be used.

  1. Click Play to view the trajectory. Afterwards, close the Trajectory Player ( in the bottom right corner of the workspacethe 3D display area in the center of the main window, where molecular structures are displayed / top right corner of the Trajectory player)

We will analyze the trajectory for properties of interest in the next Section.

6. Calculating Density and Solubility Parameters

In this section, we will analyze the results of the MD simulation from the previous section. We will focus on bulk properties, such as density and solubility parameters, of the polyethylene cell.

Figure 6-1. Opening the MS MD Trajectory Analysis panel.

  1. 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 result of the MD simulation in the previous section, amorphous poly(ethylene)
  2. Go to Tasks > Materials > Classical Mechanics > Trajectory Analysis > MS MD Trajectory Analysis
  3. Click Load from Workspace
    • The Simulation Detail tab fills with information about the system

Figure 6-2. Selecting Density and Solubility Parameter.

  1. Click the Bulk Properties tab
  2. In the drop-down menu above the first plot, select Density
  3. In the drop-down menu above the second plot, select Solubility Parameter

We may be interested in analyzing parameters from a specific portion of the trajectory. If we want to ensure that we are only looking at the trajectory from when the polyethylene cell is equilibrated, we can adjust the Trajectory Range to only include the second half of the simulation 

  1. Next to Trajectory Range, Click Set Range
    • The Trajectory Filter Panel opens

Figure 6-3. Adjusting the trajectory range.

  1. For Start frame, enter 51
  2. Click Apply
    • Review the average properties

Figure 6-4. Viewing the average properties.

  1. Compare the average properties for the full trajectory range and the limited range. We see that the full trajectory range has an average density of 0.739 g/cm3 while the average over frames 51-101 is 0.738 g/cm3. The average solubility parameter also changes minimally from full to limited frames, from 14.273 MPa1/2 to 14.278 MPa1/2. There is a very small decrease when averaging over these two ranges which means a satisfactory equilibration was achieved very quickly. 

Note: The density and solubility parameter reported above corresponds to a temperature of 400K. At 300K, which is closer to reported experimental conditions, the calculated density is ~0.82 g/cm3  and the solubility parameter is ~16.3 MPa1/2.  The data can be extracted as a PDF Report, Plots and Data using the Generate Report option

  1. Close the MS MD Trajectory Analysis panel    

7. Polymer Chain Analysis

We can further analyze the results of the MD simulation workflow carried out in Section 5 by using an additional panel, the Polymer Chain Analysis panel. The Polymer Chain Analysis panel facilitates calculation of various properties of polymer molecules from one or more MD simulations, averaged over the selected molecules and the trajectory. The panel allows for calculation of persistence length, radius of gyration, principal axes and orientational order parameter. Visit the help documentation for the approaches to calculating these various parameters. Here we will calculate the persistence length and radius of gyration for our equilibrated polyethylene cell.

Figure 7-1. Opening the Polymer Chain Analysis panel.

  1. 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 result of the MD simulation in Section 5, amorphous poly(ethylene)
  2. Go to Tasks > Materials > Classical Mechanics > Trajectory Analysis > Polymer Chain Analysis Calculations

Note: For polymer chain analysis, each structure must be the output from a Desmond simulation that has an associated trajectory.

Figure 7-2. Setting the polymer chain analysis parameters.

  1. For Define two ends, select the Polymer initiator and terminator
    • Selecting this option will define the length of the chain by the distance between the polymer chain initiator and terminator selected in Section 3
  2. For Extended chain length, select the All-trans conformer

Note: For Extended Chain Length, the User defined option can be helpful in case of very stiff polymers

  1. We will calculate the internal end-to-end distances of backbone segments. To do so, check Calculate internal distances of backbone segments
  2. Check Calculate radius of gyration
    • The radius of gyration will be calculated for each molecule and averaged over each time step

The polyethylene amorphous cell we are analyzing is made of a single monomer type, ethylene. The panel will recognize the molecules used in building the cell in this example

  1. Select Calculate Molecule Types
    • The panel recognizes that the amorphous cell is made of 100 polyethylene chains

Figure 7-3. Running polymer chain analysis.

  1. Select the Molecule type radio button
  2. Change the Job name to polymer_chain_analysis_PE
  3. Adjust the job settings () as needed
    • This job requires a CPU host. The job can be completed in less than 15 minutes on a CPU host
  4. If you would like to run the job, click Run. Otherwise, we will proceed with pre-generated results in the next step
  5. Once the job is successfully completed, a new polyethylene_cell_system (1) group, with an entry, 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 in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and is includedthe entry is represented in the Workspace, the circle in the In column is blue in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
  6. Close the Polymer Chain Analysis panel

Figure 7-4. Using the WAM to open the Polymer Chain Analysis Results.

  1. Go to File > Import Structures, navigate to the provided tutorial files and Open Section_07 > polymer_chain_analysis_PE > polymer_chain_analysis_PE-trj.cms
  2. 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 amorphous poly(ethylene)
  3. Click on the WAM button () and select Polymer Chain Analysis Results
    • The Polymer Chain Analysis Viewer panel opens
    • Alternatively, go to Tasks > Materials > Classical Mechanics > Trajectory Analysis > Polymer Chain Analysis Results

Note: In this panel, you can analyze persistence length data, radius of gyration data, and orientational order parameters, and determine the range of the trajectory over which you want various overall properties to be calculated as we did in Section 6. The range is set either by dragging the slider bars on the time series plot, or setting the start time and end time in the text boxes. The plots update automatically to show the data from the restricted time range

Figure 7-5. Viewing end-to-end distances.

First we will look at the End-to-End tab which displays analysis of end-to-end distances and values derived from the data.

  1. Set the Start time to 5. We will look at these properties within the same trajectory range as in Section 6.

The Time series plot shows that the mean end-to-end distance over each time step averages to 26.280 Å

The Molecule distribution plot shows that an end-to-end distance of ~30 Å is most frequent.

Note: You can save the calculated or derived properties along with the time range as project properties for the structure, and export the data from the time series and histogram plots to CSV files

Figure 7-6. Viewing the radius of gyration tab.

  1. Click the Radius of Gyration tab

The Time series plot shows that the mean radius of gyration is 9.962 Å

The Molecule distribution plot shows that a radius of gyration of ~11 Å is most frequent.

  1. Close the Polymer Chain Analysis Viewer panel

Proceed to explore other properties from the Polymer Chain Analysis and Viewer workflows on your own depending on your interests

8. Conclusion and References

In this tutorial, we built a styrene-butadiene copolymer chain and used the single polymer chain to construct an amorphous cell containing multiple chains. We also generated a polyethylene amorphous cell and ran an MD simulation workflow. Then, we analyzed the results of the MD simulation and further analyzed the polyethylene system with the polymer chain analysis panel.  

For further learning:

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

For further reading:

9. 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