Building Solvated Systems

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

Tutorial files

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

 

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

 

In this tutorial, we will learn to use the Solvation Builder to efficiently construct large systems in Materials Science Maestro.

 

Tutorial Content

  1. Introduction to Building Solvated Systems

  1. Creating Projects and Importing Structures

  1. Building Carbohydrates in Water

  1. Building Water on Graphene

  1. Building a Surfactant Mixture

  1. Building a Coarse-Grained Formulation

  1. Conclusion and References

  1. Glossary of Terms

1. Introduction to Building Solvated Systems

The Solvation Builder panel facilitates the construction of large, solvated systems with periodic boundary conditions in Schrödinger’s Materials Science Maestro suite. Large systems could consist of hundreds of thousands to millions of particles. The resultant structures can be used as unequilibrated inputs for subsequent molecular dynamics simulations (either all-atom or coarse-grained) with Desmond.

The Solvation Builder panel backend utilizes PackMol. Please cite PackMol in any publication that contains results from the use of this panel (see References).

With respect to constructing large systems with periodic boundary conditions, the Solvation Builder can be used in tandem with, or instead of, the Disordered System Builder depending on the requirements of the study. The use cases for one panel versus the other will be discussed throughout this tutorial.

Note that this tutorial does not cover the Disordered System Builder or the steps for subsequent molecular dynamics simulation using the Molecular Dynamics (MD) Multistage Workflow panel. Background information on these topics may be useful for working through this tutorial, and is available in the Disordered System Building and Molecular Dynamics Multistage Workflows tutorial.

Herein, we will study four examples of constructing large systems; (1) in Section 3 we will build a ~300,000 atom box containing amylose and water, (2) in Section 4 we will build a ~300,000 atom box of water molecules on a graphene sheet, (3) in Section 5 we will build a ~700,000 atom box of a mixture of surfactants, and (4) in Section 6 we will build a ~400,000 particle box containing coarse-grained components of an ibuprofen-cyclodextrin model pharmaceutical formulation.

outputs of the systems to be covered in this tutorial

2. Creating Projects and Importing Structures

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

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

  1. Double-click the Materials Science icon

Figure 2-1. Change Working Directory option.

  1. Go to File > Change Working Directory
  2. Find your directory, and click Choose
  3. Pre-generated files are included for running jobs or examining output. Download the zip file here: schrodinger.com/sites/default/files/s3/release/current/Tutorials/zip/solvation_builder.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 solvation_builder_tutorial, click Save
    • The project is now named solvation_builder_tutorial.prj

Figure 2-3. Importing the provided structures.

The input molecules for the four systems constructed in this tutorial are all provided.

  1. Go to File > Import Structures…
  2. Navigate to where you downloaded the provided files (presumably in your Working Directory), choose input_molecules.maegz and click Open

Figure 2-4. The entry list after importing.

Fourteen structures are added to the entry list, grouped by Section of the tutorial. Feel free to visualize the various components.

For practicing generating these structures on your own, please see the following educational resources:

3. Building Carbohydrates in Water

In this section, we will use the Solvation Builder panel to construct a system containing 10 amylose chains in 100,000 water molecules, a system of >300,000 atoms.

Figure 3-1. Including the carbohydrate and selecting the solvent in the entry list.

  1. Include the poly(alpha-D-Glucose) entry and select the water entry

Figure 3-2. The Solvation Builder panel.

  1. Go to Tasks > Materials > Structure Builders > Solvate System
    • The Solvation Builder panel opens
    • Ensure that water is the only entry listed in the Component table. If other entries are shown, return to the previous step

Let’s learn about the settings and capabilities of the Solvation Builder panel.

The Solvation tab is used to specify the Solute and Solvent, as well as various parameters for the build (cell dimensions, solute placement, component quantities).

Solute

  • We define the solute as the molecule or collection of molecules to be solvated
  • A Solute must be loaded from the workspace from the included entry. In this first example, the included carbohydrate structure will be the solute.
  • The Solute can be non-periodic or periodic
  • Note that while the term “solute” is used here, we will also load substrates in this way (for example, see Section 4).
  • In order to load multiple, unique Solute structures, a single entry should be prepared with various molecules, for example, using the Disordered System Builder panel or by simply generating a single entry with several molecules (there is a useful merge capability within the entry list - just be sure to separate the molecules in space after merging). In this approach,  the geometry of the multiple structures (and their relative orientations) will be maintained in the output structure from the Solvation Builder
  • Once a Solute is loaded, it can be positioned in the cell using the Positioning options. The amount of molecules can be specified with the Number of molecules input. Note, though, that while the Solute will be placed in arbitrary x, y and z directions, its conformation will not be altered in any way during the build (i.e. it will be placed in the exact conformation that was provided as input)

Cell Buffer & Cell Dimensions

  • If a periodic system is loaded as substrate, the Cell dimensions will populate with the dimensions of the loaded periodic system (for example, see Section 4). In that case, the Cell Buffer inputs can be used to add to the a, b or c dimensions of the input cell if desired.
  • If a non-periodic system is loaded as substrate, the Cell dimensions must be manually populated (the Cell buffer will not be used).
  • The Total density box at the bottom of the cell can be used to crudely assist in the determination of cell dimensions. Generally, we should aim to build systems of low density (for example, 0.4-0.5 g/cm3 for a water-based system) in order to generate the quickest build. Of course, the output system should then be passed to Desmond for equilibration via molecular dynamics simulation, for example, via the Molecular Dynamics (MD) Multistage Workflow panel.

Components Table

  • The Components table operates the same as the corresponding section in the Disordered System Builder panel.
  • The Guess Composition button can be used to scale the ratio of molecules in the table proportional to their weight percentages towards a density of ~1 g/cm3.

Finally, the Force field tab is used to optionally assign a force field. For an all-atom system, OPLS4 is available and can be customized as usual. For a coarse-grained system, a force-field must be selected (for example, see Section 6). Note that the Force field tab directly resembles the capabilities of the Prepare for Molecular Dynamics panel.

For a complete description of the Solvation Builder panel, please visit the help documentation.

Figure 3-3. Parameterizing the Solvation Builder panel.

  1. Click Load from Workspace
    • poly(alpha-D-Glucose) appears next to the button, indicating that the entry has been loaded into the panel. Because the entry is not periodic, Non-fixed is selected by default
  2. For Number of molecules input 10
  3. Below, in the Components Table, for Number of molecules, input 100000
    • Because water is the only component, the number of water molecules should also update to 100000
  4. Set the Cell dimensions to 200 x 200 x 200
    • Note that the density updates accordingly. These dimensions were chosen to target a low-density structure for an optimal build. Building a higher density system will result in a significantly longer build, or non-convergence.
  5. Change the Job name to solvation_builder_carbohydrate_water
  6. Adjust the job settings () as needed
    • This job requires a CPU host. The job can be completed in about 15 minutes on a CPU host with 1 processor
  7. If you would like to run the job, click Run. Otherwise, import the provided output via Section_03 > solvation_builder_carbohydrate_water > solvation_builder_carbohydrate_water-out.maegz
  8. Close the Solvation Builder panel
    • The Solvation Builder panel is interactive with the workspace and entry list, so it is always a good idea to close the panel after working with it

Figure 3-4. The output structure in the workspace.

When the job finishes, or after importing, feel free to visualize the output structure. In the figure, the amylose molecules have been changed to CPK representation for ease of visualization.

 

In practice, this structure should now be passed to Desmond for molecular dynamics simulation, for example, via the Molecular Dynamics (MD) Multistage Workflow panel.

  1. Use the WAM (workflow action menu) button (Click to Expand) to open the MD Multistage Workflow panel
    • Alternatively, access the panel via Tasks > Materials > Classical Mechanics > MD Simulations > MD Multistage Workflow

 

If so, it is recommended to use the Force field tab to force-field-type the structure. Alternatively, pass the output to the Prepare for Molecular Dynamics panel. 

Note that this exact structure could also be built with the Disordered System Builder panel. In this case, the Solvation Builder is more efficient. See the Building a Carbohydrate Polymer tutorial for steps for building a similar system.

4. Building Water on Graphene

In this section, we will use the Solvation Builder panel to construct a system containing 100,000 water molecules on a graphene sheet, a system of >300,000 atoms.

Figure 4-1. Including the nanosheet and selecting the solvent in the entry list.

  1. Include the nanosheet entry and select the water entry

Figure 4-2. The Solvation Builder panel.

  1. Go to Tasks > Materials > Structure Builders > Solvate System
    • The Solvation Builder panel opens
    • Ensure that water is the only entry listed in the Component table. If other entries are shown, return to the previous step
    • If you performed the steps in the previous section, reset the panel using the reset button ()

Figure 4-3. Parameterizing the Solvation Builder panel.

  1. Click Load from Workspace
    • nanosheet appears next to the button, indicating that the entry has been loaded into the panel
    • Because the system is periodic, the Positioning is Fixed by default
  2. Below, in the Components Table, for Number of molecules, input 100000
    • Because water is the only component, the number of water molecules should also update to 100000
  3. In the Cell buffer input, for c, input 1200
    • Notice that the Cell dimensions update from the original dimensions of the graphene sheet to now have an addition 1200 Å in the c direction
    • Note that the density updates accordingly. These dimensions were chosen to target a low-density structure for an optimal build. Building a higher density system will result in a significantly longer build, or non-convergence.
  4. Change the Job name to solvation_builder_graphene_water
  5. Adjust the job settings () as needed
    • This job requires a CPU host. The job can be completed in about 5 minutes on a CPU host with 1 processor
  6. If you would like to run the job, click Run. Otherwise, import the provided output via Section_04 > solvation_builder_graphene_water > solvation_builder_graphene_water-out.maegz
  7. Close the Solvation Builder panel
    • The Solvation Builder panel is interactive with the workspace and entry list, so it is always a good idea to close the panel after working with it

Figure 4-4. The output structure in the workspace.

When the job finishes, or after importing, feel free to visualize the output structure.

 

This structure should now be passed to Desmond for molecular dynamics simulation, for example, via the Molecular Dynamics (MD) Multistage Workflow panel.

  1. Use the WAM button (Click to Expand) to open the MD Multistage Workflow panel
    • Alternatively, access the panel via Tasks > Materials > Classical Mechanics > MD Simulations > MD Multistage Workflow

 

 

If so, it is recommended to use the Force field tab to force-field-type the structure. Alternatively, pass the output to the Prepare for Molecular Dynamics panel. 

Note that this exact structure could also be built with the Disordered System Builder panel. In this case, Solvation Builder is more efficient. See the Building a Polymer-Polymer Interface Model tutorial for steps for building a similar system.

5. Building a Surfactant Mixture

In this section, we will use the Solvation Builder panel to construct a system containing a mixture of surfactants in water, a system of >700,000 atoms. The system will contain aqueous sodium dodecyl sulfate (SDS) and zwitterionic lauramidopropyl betaine (LAPB), which are two surfactants commonly found in cosmetic and personal care products.

Figure 5-1. Including the SDS_anion and selecting the remaining solvent in the entry list.

  1. Include the SDS_anion entry and select the sodium_cation, LAPB_cation, hydroxide_anion and water entries.

 

Here, there are multiple components that one might consider the solute versus the solvent. We arbitrarily select SDS_anion as our solute.

Figure 5-2. The Solvation Builder panel.

  1. Go to Tasks > Materials > Structure Builders > Solvate System
    • The Solvation Builder panel opens
    • Ensure that four components are listed in the Component table. If not, return to the previous step
    • If you performed the steps in the previous section, reset the panel using the reset button ()

Figure 5-3. Parameterizing the Solvation Builder panel.

  1. Click Load from Workspace
    • SDS_anion appears next to the button, indicating that the entry has been loaded into the panel
    • Because the entry is not periodic, Non-fixed is selected by default
  2. For Number of molecules input 500
  3. Below, in the Components Table, for Number of molecules, input 200000
    • For sodium_cation input 500
    • For LAPB_cation input 1500
    • For hydroxide_anion input 1500
    • For water input 196500
  4. Set the Cell dimensions to 240 x 240 x 240
    • Note that the density updates accordingly. These dimensions were chosen to target a low-density structure for an optimal build. Building a higher density system will result in a significantly longer build, or non-convergence.
  5. Change the Job name to solvation_builder_surfactants
  6. 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 with 1 processor
  7. If you would like to run the job, click Run. Otherwise, import the provided output via Section_05 > solvation_builder_surfactants > solvation_builder_surfactants-out.maegz
  8. Close the Solvation Builder panel
    • The Solvation Builder panel is interactive with the workspace and entry list, so it is always a good idea to close the panel after working with it

Figure 5-4. The output structure in the workspace.

When the job finishes, or after importing, feel free to visualize the output structure. Note that in the Figure, the water molecules are hidden for ease of visualization.

 

In practice, this structure should now be passed to Desmond for molecular dynamics simulation, for example, via the Molecular Dynamics (MD) Multistage Workflow panel.

  1. Use the WAM button (Click to Expand) to open the MD Multistage Workflow panel
    • Alternatively, access the panel via Tasks > Materials > Classical Mechanics > MD Simulations > MD Multistage Workflow

 

 

If so, it is recommended to use the Force field tab to force-field-type the structure. Alternatively, pass the output to the Prepare for Molecular Dynamics panel. 

Note that this exact structure could also be built with the Disordered System Builder panel. In this case, Solvation Builder is more efficient. See the Disordered System Building and Molecular Dynamics Multistage Workflows tutorial for steps for building a similar system.

6. Building a Coarse-Grained Formulation

In this section, we will use the Solvation Builder panel to construct a coarse-grained system containing beta-cyclodextrin (β-CD), deprotonated ibuprofen, sodium cations and water, a system of >400,000 particles. For complete details on this system, please refer to the Ibuprofen Cyclodextrin Inclusion Complexes with the Martini Coarse-Grained Force Field tutorial.

Figure 6-1. Including the BCD_cg structure and selecting the remaining solvent in the entry list.

  1. Include the BCD_cg entry and select the Na_ion, WF_water, W_water and ibuprofen entries.

 

Here, there are multiple components that one might consider the solute versus the solvent. We arbitrarily select BCD_cg as our solute.

Figure 6-2. The Solvation Builder panel.

  1. Go to Tasks > Materials > Structure Builders > Solvate System
    • The Solvation Builder panel opens
    • Ensure that four components are listed in the Component table. If not, return to the previous step
    • If you performed the steps in any of the previous sections, reset the panel using the reset button ()

Figure 6-3. Parameterizing the Solvation Builder panel.

  1. Click Load from Workspace
    • BCD_cg appears next to the button, indicating that the entry has been loaded into the panel
    • Because the entry is not periodic, Non-fixed is selected by default
  2. For Number of molecules input 464
  3. Below, in the Components Table, for Number of molecules, input 400640
    • For Na_ion input 320
    • For WF_water input 40000
    • For W_water input 360000
    • For ibuprofen input 320
  4. Set the Cell dimensions to 750 x 750 x 750
    • Note that the density updates accordingly. These dimensions were chosen to target a low-density structure for an optimal build. Building a higher density system will result in a significantly longer build, or non-convergence.
  5. Change the Job name to solvation_builder_formulation
  6. Adjust the job settings () as needed
    • This job requires a CPU host. The job can be completed in about 15 minutes on a CPU host with 1 processors
  7. If you would like to run the job, click Run. Otherwise, import the provided output via Section_06 > solvation_builder_formulation > solvation_builder_formulation-out.maegz
  8. Close the Solvation Builder panel
    • The Solvation Builder panel is interactive with the workspace and entry list, so it is always a good idea to close the panel after working with it

Figure 6-4. The output structure in the workspace.

When the job finishes, or after importing, feel free to visualize the output structure.

 

In practice, this structure should now be passed to Desmond for molecular dynamics simulation, for example, via the Molecular Dynamics (MD) Multistage Workflow panel.

  1. Use the WAM button (Click to Expand) to open the MD Multistage Workflow panel
    • Alternatively, access the panel via Tasks > Materials > Classical Mechanics > MD Simulations > MD Multistage Workflow

For practice force-field-typing coarse-grained structures, see the Ibuprofen Cyclodextrin Inclusion Complexes with the Martini Coarse-Grained Force Field tutorial.

Note that this exact structure could also be built with the Disordered System Builder panel. In this case, Solvation Builder is more efficient. See the Ibuprofen Cyclodextrin Inclusion Complexes with the Martini Coarse-Grained Force Field tutorial for steps for building a similar system.

7. Conclusion and References

In this tutorial, we learned how to use the Solvation Builder to efficiently construct large systems in Materials Science Maestro.

For further learning:

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

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

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

For further reading:

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