Disordered System Building and Molecular Dynamics Multistage Workflows

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

Tutorial files

0.7 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 Disordered System Builder and Molecular Dynamics (MD) Multistage Workflow panels to build and equilibrate model systems.

 

Tutorial Content

  1. Introduction to Disordered System Building

  1. Introduction to MD Multistage Workflows

  1. Creating Projects and Importing Structures

  1. Building and Running MD for a Single Component Box

  1. Building and Running MD for a Multi-Component Box

  1. Building and Running MD for a Multi-Component Box with Ions

  1. Conclusion and References

  1. Glossary of Terms

1. Introduction to Disordered System Building

The Disordered System Builder panel facilitates building a randomized multi-component mixture of a given composition, either on its own, or on a substrate. Each component corresponds to an entry, which could be a molecule, ion or more complex cluster of molecules. The components should all be either all-atom or coarse-grained. The builder allows you to select the quantity and proportion of each component, as well as specify how the initial box (or cell, used interchangeably herein) is constructed. The output structure is an unequilibrated starting point that can be used for subsequent molecular dynamics (MD) simulations.

Three common use cases for the panel are:

a) constructing a box of a single component (demonstrated in Section 4)

b) constructing a box of multiple components (demonstrated in Section 5 and Section 6)

c) constructing a more complex interfacial or immersed system involving substrates (demonstrated in the Building a Polymer-Polymer Interface Model and Building a Carbohydrate Polymer tutorials, for example)

In this tutorial, we will use the Disordered System Builder panel to construct three systems in preparation for MD Multistage Workflows: a single component box of CBP (4,4’-bis(N-carbazolyl)-1,1’-biphenyl), a multi-component box of water and polyethylene glycol and a multi-component box of sodium lauryl ether sulfate (SLES) and water.

If constructing very large, solvated systems, consider alternatively using the Solvation Builder.

2. Introduction to Molecular Dynamics Multistage Workflows

A molecular dynamics simulation workflow may be composed of several stages, including but not limited to Brownian dynamics, molecular dynamics, simulated annealing or analysis. The MD Multistage Workflow panel facilitates the automation of several MD stages in which the results of each stage are used as inputs for the next stage, including the final velocities.

An example workflow could be summarized as follows:

In Materials Science Maestro, MD simulations are fueled by the backend engine Desmond with the default OPLS4 force field (with extensive capabilities for customization as needed). For a complete introduction to Desmond, visit the thorough help documentation. 

MD is the fundamental computational methodology that underlies many workflows in Materials Science Maestro, particularly in the areas of Polymeric Materials and Pharmaceutical Formulations, but also in Organic Electronics and other major applications. See the Conclusion and References section at the end of the tutorial to access additional related educational materials utilizing MD.

In this tutorial, we will learn the basics of using the MD Multistage Workflow panel by running MD simulations on the three boxes prepared with the Disordered System Builder. We will view the output trajectories from the simulations and analyze the bulk system. These steps are fundamental to any workflow involving MD simulation.

3. 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 3-1. 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/dosb_md.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 3-2. Save Project panel.

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

Figure 3-3. Five entries in the entry list to be used as the components in the subsequent sections.

We will proceed to import the components that we will use in the subsequent sections: CBP, a polyethylene glycol 10-mer, water, sodium cation and lauryl ether sulfate anion. If you would prefer to draw or build these components yourself using the 2D Sketcher and the Polymer Builder, feel free to do so following similar steps outlined in the Introduction to Materials Science Maestro tutorial. Otherwise:

  1. Go to File > Import Structures
  2. Navigate to where you have downloaded the provided files (presumably in your working directorythe location where files are saved), and choose the components.mae file
  3. Click Open
    • A new entry group is added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion entitled components (5) containing the five entries

4. Building and Running MD for a Single Component Box

In this section, we will build a single component box with the Disordered System Builder panel containing 300 molecules of CBP. We will then use the MD Multistage Workflow panel to perform a molecular dynamics simulation and subsequent analysis on the system. This workflow can be utilized for preparing a box containing any organic molecule. Here, we have chosen CBP because it is a prototypical OLED host material, which is studied further in the Molecular Deposition tutorial. To learn more about MD calculations watch Getting Going with Materials Science Maestro Video Series: All-Atom Molecular Dynamics.

Figure 4-1. The CBP entry selected and the Disordered System Builder panel open.

  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 only the CBP entry from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
    • Recall that 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 means to highlight from 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
    • The Disordered System Builder panel opens
    • Because the CBP entry was 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, it is populated as the only component by default. If you see different components or additional components, revisit Step 1

The first section of the Components tab is called the Components table and it is used to specify the structures to be included in the box, as well as their quantities and proportions. Note that the Components table updates interactively.

The Substrate section of the Components tab is for placing the disordered mixture on a substrate (immersed, container or a planar interface). This functionality is not demonstrated in this tutorial, though it is taught in the Building a Polymer-Polymer Interface Model and Building a Carbohydrate Polymer tutorials.

The Periodic Boundary Conditions (PBC) section allows you to specify the nature of the output periodic cell if you wish.

Read more in the detailed help documentation.

Figure 4-2. The Components tab.

In this case, we simply wish to construct a one component system of 300 molecules:

  1. For Initial state, choose Tangled chain
    • Visit the documentation for the differences between the choices. Typically, tangled chain allows for the quickest build

Note: Note that the build is just a starting cell, it is going to be subsequently equilibrated with MD. Accordingly, here we choose settings for a relatively quick build

  1. For Number of molecules, input 300
    • The number of CBP molecules updates in real-time
    • Typically, a system size of 10,000 atoms or more is used for MD. Systems of size 20,000-50,000 atoms are typical for ‘production’ runs. Larger systems are possible, but will take substantially longer to run. In this example, 300 molecules of CBP will be a 18,600 atom system

 

Note: The Cells Tab is for specifying the type and number of boxes to create. In this case, we are only generating one replicate, and we (as is almost always the case) intend to use the output for an MD simulation, so the defaults are maintained. It also includes the setting to ensure that the output is ‘prepared’ for MD with a specific force field option. The default option is OPLS4 and is recommended for most systems. OPLS5 with polarizability on select chemical groups is available but it is recommended to confirm first if it is suitable for the system and property of interest given simulation time difference between OPLS5 and OPLS4. It is recommended to use OPLS4 for initial relaxation for any newly built structures. Vacuum or void space may cause OPLS5 convergence failure.

Note: Machine Learning Force Fields (MLFF) are available as an alternative to OPLS force fields. Additional information regarding MLFF can be found in the help documentation or on our website.

Note: The defaults are good choices in the Disorder Tab, again recognizing that this will be followed with MD. Generally, it is recommended to build initial systems to a density that is lower than the expected equilibrated density, allowing the subsequent MD protocol to compress the system. A full summary of the Disorder Tab and the Disorder Options can be found in the documentation.

Figure 4-3. The Disorder tab and running the job.

  1. Change the Job name to disordered_system_CBP
  2. Adjust the job settings () as needed
    • This job requires a CPU host. The job can be completed in about 30 minutes on a CPU host
  3. If you would like to run the job yourself, click Run. Otherwise, import the pregenerated Section_04 > disordered_system_CBP > disordered_system_CBP_system-out.cms file from the provided tutorial files via File > Import Structures
    • 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
  4. Close the Disordered System Builder

Note: In general, always close the Disordered System Builder after use. This panel is interactive with the workspace and leaving it open can cause slowdowns

Figure 4-4. Output of the Disordered System Build.

  1. When the job is finished or after importing, 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 disordered_system_CBP_all_components_amorphous from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion

Figure 4-5. Opening the MD Multistage Workflow panel via the WAM button.

MD simulations in MS Maestro are performed with the MD Multistage Workflow panel.

  1. Use the WAM (workflow action menu) button () to open the MD Multistage Workflow panel
    • Alternatively, access the panel via 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 (Materials relaxation, Bulk macromolecule relaxation, Compressive, Ladder polymer relaxation, OPLS5 drude convergence, Relaxation1, Rigorous compression, Semicrystal relaxation 1, Semicrystal relaxation 2, Constant pressure, Constant volume, Martini, Constant Volume Martini, Repulsive harmonic) 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.

 

 

Here we will use a relatively standard simulation protocol to equilibrate the system. First, the Compressive relaxation protocol will be applied, which is a seven step workflow that is effective for compressing systems that are built to low density. This relaxation protocol includes a high pressure stage intended to compress the system. Subsequently, we will implement an MD stage at constant temperature and pressure to equilibrate the cell and gather trajectory data for analysis. 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 4-6. Setting up the MD Multistage Workflow.

  1. Check Relaxation protocol and choose Compressive
  2. Change the next stage (Stage 8) to Molecular Dynamics
  3. Set the Simulation time (ns) to 10
  4. Set the Trajectory Recording interval (ps) to 200
    • This will generate 50 frames in the trajectory
  5. Click Append Stage
    • A 9th stage appears in the workflow
  6. Change the new stage (Stage 9) to Analysis
  7. Change the Job name to multistage_simulation_CBP
  8. Adjust the job settings () as needed
    • This job requires a GPU host. The job can be completed in about 3 hours on a GPU host
  9. If you would like to run the job yourself, click Run. Otherwise, import the pre-generated Section_04 > multistage_simulation_CBP > multistage_simulation_CBP-out.cms file from the provided tutorial files via File > Import Structures
  10. Close the MD Multistage Workflow panel

Figure 4-7. Output of the MD simulation.

  1. When the job is finished or after importing, 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 new disordered_system_CBP_all_components_amorphous entry from the entry list

Figure 4-8. Viewing the trajectory.

  1. 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

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.

 

  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)

Figure 4-9. Loading data into the MS MD Trajectory Analysis panel.

Finally, we can view bulk properties of the system over the course of the trajectory:

  1. Go to Tasks > Materials > Classical Mechanics > Trajectory Analysis > MS MD Trajectory Analysis
  2. Click Load from Workspace
    • The Simulation Detail tab fills with information about the MD job and system

Figure 4-10. Viewing bulk properties.

  1. Go to the Bulk Properties tab
  2. Use the dropdowns to view the various properties as a function of time from the MD stage
    • Density and Solubility parameter are shown in the Figure
  3. When you are finished, close the MS MD Trajectory Analysis panel

In practice, depending on your research goals, you may now wish to revisit your parameters for the MD Multistage Workflow. For example, you may wish to run a more ‘production’ level MD simulation with a longer simulation time or larger box. You may also proceed to use this equilibrated cell as a starting point for subsequent workflows. For example, in the Molecular Deposition tutorial, this CBP box is used as the substrate for a simulated deposition procedure. Note that some workflows have MD stages built-in, whereas others require equilibrated cells as inputs. Always refer to the help documentation when performing a new workflow.

5. Building and Running MD for a Multi-Component Box

In this section, we will build a multi-component box with the Disordered System Builder panel containing 36 10-mers of PEG and 1464 molecules of water, representing a ~40 wt% PEG solution. We will then use the MD Multistage Workflow panel to perform a molecular dynamics simulation. This workflow can be utilized for preparing a box containing any mixture of molecules. Here, we choose PEG and water because it is a prototypical solution of interest.

If you already built this simulation box in the Introduction to Materials Science Maestro tutorial, you can skip to Step 11 to proceed with the MD simulation.

Figure 5-1. The entries selected and the Disordered System Builder panel open.

  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 PEG_10mer and water entries from the entry list
  2. Go to Tasks > Materials > Structure Builders > Disordered System
    • The Disordered System Builder panel opens
    • The two selected components are by default loaded into the panel
    • If you see different components or additional components, revisit Step 1

Figure 5-2. Setting the components and running the job.

  1. For Initial state, choose Tangled chain
  2. Change Number of molecules to 1500
  3. In the Components table, change the Molecules for water to 1464 and PEG to 36
    • The wt% appears in the panel and the table updates interactively
    • The total number of molecules was selected to generate a reasonable size box for an MD simulation
    • Recall that typically a system size of 10,000 atoms or more is used for MD. Systems of size 20,000-50,000 atoms are typical for ‘production’ runs. Larger systems are possible, but will take substantially longer to run. This system will contain ~7000 atoms, which is small but sufficient for this simple system and for learning purposes
  4. Change the Job name to disordered_system_PEG_water

 

This job will take about 3 minutes on a CPU host. To adjust job settings, click on the gear () button next to the Job name. If you would like to run the job yourself, click Run. Otherwise, import the pregenerated Section_05 > disordered_system_PEG_water > disordered_system_PEG_water_system-out.cms file from the provided tutorial files via File > Import Structures

 

  1. Close the Disordered System Builder

 

Figure 5-3. Output of the Disordered System Builder in the workspace.

When the job is complete, a new entry group will be incorporated titled MD: disordered_system_PEG_water_system (1) containing one entry titled disordered_system_PEG_water_all_components_amorphous

  1. Includethe entry is represented in the Workspace, the circle in the In column is blue the new entry
    • The box is visible in the workspace
    • The components are colored by default, but feel free to stylize as you wish
  2. Use the WAM button () to open the MD Multistage Workflow panel
    • Alternatively, access the panel via Tasks > Materials > Classical Mechanics > MD Simulations > MD Multistage Workflow

We will next equilibrate this disordered system in order to prepare it for an MD simulation at constant volume. This method is useful for preparing input structures for calculation methods that use constant volume ensembles (e.g. viscosity) or impose prescribed changes to the input cell (e.g. elastic constants).

First, the Materials relaxation protocol will be applied, which is a robust three-stage scheme for equilibrating materials. Since this system is largely composed of liquid water, the high pressure stage used in the Compressive protocol (as implemented in Section 4) will not be necessary, however the Compressive protocol would still give a well equilibrated cell. Next, the system will be equilibrated using MD in the isothermal-isobaric (NPT) ensemble. This step will be used to create a trajectory for determining the average size of the simulation cell, and thus the average density of the system. Subsequently, an Average Cell stage will be used to determine the average cell size from the trajectory created in the previous step, and apply it to the system. Finally, a simulation will be performed using MD in the isothermal-isochoric (NVT) ensemble.

Figure 5-4. Setting up the MD Multistage Workflow.

  1. Check Relaxation protocol and choose Materials relaxation
  2. Change the next stage (Stage 4) to Molecular Dynamics
  3. Set the Simulation time (ns) to 10
  4. Set the Trajectory Recording interval (ps) to 200
  5. Click Append Stage
    • A 5th stage appears in the workflow
  6. Change the new stage (Stage 5) to Average Cell
  7. Click Append Stage
    • A 6th stage appears in the workflow
  8. Change the new stage (Stage 6) to Molecular Dynamics
  9. Set the Simulation time (ns) to 10
  10. Set the Trajectory Recording interval (ps) to 200
  11. Change the Ensemble class to NVT
  12. Change the Job name to multistage_simulation_PEG_H2O
  13. Adjust the job settings () as needed
    • This job requires a GPU host. The job can be completed in about 3 hours on a GPU host
  14. If you would like to run the job yourself, click Run. Otherwise, import the pre-generated Section_05 > multistage_simulation_PEG_H2O > multistage_simulation_PEG_H2O-out.cms file from the provided tutorial files via File > Import Structures
  15. Close the MD Multistage Workflow panel

Figure 5-5. Output of the MD simulation.

  1. When the job is finished or after importing, 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 new disordered_system_PEG_H2O_all_components_amorphous entry from the entry list

 

As we did in Section 4, proceed to visualize the Trajectory if you are interested. You can also analyze the density profile of the cell using the Density Profile panel accessible from Tasks > Materials > Tools. In this case, because we did not perform an analysis stage, we cannot use the MS MD Trajectory Analysis panel, but we can get similar information from the Simulation Quality Analysis panel by loading in the .ene file

6. Building and Running MD for a Multi-Component Box with Ions

In this section, we will build a multi-component box with the Disordered System Builder panel containing 244 SLES molecules (244 sodium cations and 244 lauryl ether sulfate anions) and 8220 molecules of water, representing a ~40 wt% SLES solution. We will then use the MD Multistage Workflow panel to perform a molecular dynamics simulation. Here, we choose SLES and water because it is a prototypical surfactant solution of interest, introduces how to handle ions in a disordered system and it is studied further in the Calculating Surfactant Tilt and Electrostatic Potential of a Bilayer System tutorial.

Our simulation box is going to contain three components which are shown below: lauryl ether sulfate (the anionic component of the SLES-3 derivative, where 3 designates the number of ethoxy linkers), sodium cation and water.

Figure 6-1. The entries selected and the Disordered System Builder panel open.

  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 sodium_cation, LES_anion and water entries from the entry list

 

Note: For systems containing charged particles, it is generally a best practice to separate the anion and cation components into separate entries, as we have done here. To be sure that charges are assigned, you can open the 2D Sketcher or add charge labels in the workspace. For detailed instructions, the complete steps for drawing these specific inputs are provided in the Calculating Surfactant Tilt and Electrostatic Potential of a Bilayer System tutorial.

  1. Go to Tasks > Materials > Structure Builders > Disordered System
    • The Disordered System Builder panel opens
    • The three selected components are by default loaded into the panel
    • If you see different components or additional components, revisit Step 1

Figure 6-2. Setting the components and running the job.

  1. For Initial state, choose Tangled chain
  2. Change Number of molecules to 8708
  3. In the Components table, change the Molecules for water to 8220, sodium_cation to 244 and LES_anion to 244
    • The wt% appears in the panel and the table updates interactively
    • The total number of molecules was selected to generate a reasonable size box for an MD simulation
    • Recall that typically a system size of 10,000 atoms or more is used for MD. Systems of size 20,000-50,000 atoms are typical for ‘production’ runs. Larger systems are possible, but will take substantially longer to run. This system will contain ~40,000 atoms

Note: For systems with ions, it is essential that the component quantities balance the charges. In other words, the overall cell must be neutral.

  1. Change the Job name to disordered_system_SLES_water

 

This job will take about 5 minutes on a CPU host. To adjust job settings, click on the gear () button next to the Job name. If you would like to run the job yourself, click Run. Otherwise, import the pregenerated Section_06 > disordered_system_SLES_water > disordered_system_SLES_water_system-out.cms file from the provided tutorial files via File > Import Structures

  1. Close the Disordered System Builder

Figure 6-3. Output of the Disordered System Builder in the workspace.

When the job is complete, a new entry group will be incorporated titled MD: disordered_system_SLES_water_system (1) containing one entry titled disordered_system_SLES_water_all_components_amorphous

  1. Includethe entry is represented in the Workspace, the circle in the In column is blue the new entry
    • The box is visible in the workspace
    • The components are colored by default, but feel free to stylize as you wish
  2. Use the WAM button () to open the MD Multistage Workflow panel
    • Alternatively, access the panel via Tasks > Materials > Classical Mechanics > MD Simulations > MD Multistage Workflow

Here we will use a relatively standard simulation protocol to equilibrate the system, similar to that which was used in Section 4. Since this system is largely composed of liquid water, either the Materials relaxation protocol or the Compressive relaxation protocol could be effectively applied. For this example let’s choose the Compressive relaxation protocol, which is a seven step workflow that is effective for compressing systems that are built to low density. This relaxation protocol includes a high pressure stage intended to densify the system. Subsequently, we will implement an MD stage at constant temperature and pressure to equilibrate the cell and gather trajectory data for analysis. We will use a 100 ns simulation time to ensure enough time for the system to equilibrate to a reasonable macrostructure. 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 6-4. Setting up the MD Multistage Workflow.

  1. Check Relaxation protocol and choose Compressive
  2. Change the next stage (Stage 8) to Molecular Dynamics
  3. Set the Simulation time (ns) to 100
  4. Set the Trajectory Recording interval (ps) to 1000
    • This will generate 100 frames in the trajectory
  5. Click Append Stage
    • A 9th stage appears in the workflow
  6. Change the new stage (Stage 9) to Analysis
  7. Change the Job name to multistage_simulation_SLES_water
  8. Adjust the job settings () as needed
    • This job requires a GPU host. The job can be completed in about 24 hours on a GPU host
  9. If you would like to run the job yourself, click Run. Otherwise, import the pre-generated Section_06 > multistage_simulation_SLES_water > multistage_simulation_SLES_water-out.cms file from the provided tutorial files via File > Import Structures
  10. Close the MD Multistage Workflow panel

Figure 6-5. Output of the MD simulation.

  1. When the job is finished or after importing, 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 new disordered_system_SLES_water_all_components_amorphous entry from the entry list

Figure 6-6. Output of the MD simulation after stylizing the surfactant anions and increasing the extents.

As we did in Section 4, proceed to visualize the trajectory and bulk properties of the cell if you are interested. You can also analyze the density profile of the cell using the Density Profile panel.

In addition, you may be interested in exploring the Structure Factor for this system.

In this case, micellar aggregation is observed in the output of the MD simulation, which can be most easily visualized by changing the representation of the lauryl ether sulfate anions and extending extents (shown in the Figure).

In the Calculating Surfactant Tilt and Electrostatic Potential of a Bilayer System tutorial, we revisit a closely related system, and use a different building approach to generate a bilayer. 

Note that an alternative approach to constructing this system is demonstrated in the Building Solvated Systems tutorial. The Solvation Builder, detailed therein, is another useful builder tool, particularly for constructing very large (100,000s - 1,000,000s of particles) systems.

7. Conclusion and References

In this tutorial, we learned how to use the Disordered System Builder and MD Multistage Workflow panels to build and equilibrate model systems.

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.

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8. 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