Building a Coarse-Grained Polymer Model using Dissipative Particle Dynamics

Tutorial Created with Software Release: 2026-1
Topics: Consumer Packaged Goods, Pharmaceutical Formulations, Polymeric Materials
Methodology: Coarse-Grained Modeling
Products Used: Desmond, MS CG, MS Maestro

Tutorial files

8.3 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:

 

This tutorial demonstrates how to build a coarse-grained polymer chain and construct an amorphous cell with the coarse-grained chain, for use in a dissipative particle dynamics simulation.

 

Tutorial Content

  1. Creating Projects and Importing Structures

  1. Generating Coarse-Grained Molecules

  1. Applying a Coarse-Grained Force Field

  1. Relaxing and Equilibrating Structures

  1. Appendix - Calculating Parameters

  1. Conclusion and References

  1. Glossary of Terms

1. 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 1-1. Change Working Directory option.

  1. Go to File > Change Working Directory, find your directory
  2. Click Choose
  3. Pre-generated input and results 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_coarsegrained.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 1-2. Save Project.

  1. Go to File > Save Project As
  2. Change the File name to Build_CoarseGrained
  3. Click Save
    • The project is now named Build_CoarseGrained.prj

2. Generating Coarse-Grained Molecules

A coarse-grained model relates all-atom molecules and portions of molecules to beads. The desired mapping of the all-atom system to the coarse-grained can be determined by evaluation of model goals and the underlying molecular system. To build coarse-grained models, the desired mapping must be known, as well as all associated parameters. In this tutorial, we will use the Coarse-Grained Sketcher to build a polyisoprene/polystyrene block copolymer chain for use in a dissipative particle dynamics (repulsive harmonic) study.

2.1 Create a polyisoprene/polystyrene block copolymer chain

Figure 2-1. Add a New Site.

  1. Go to Tasks > Materials > Classical Mechanics > Coarse Grain Models > Coarse-Grained Sketcher under Coarse-Grained Modeling
    • The Coarse-Grained Sketcher opens

Note: Click the stars next to items in the Tasks toolbar to add them to your Favorites toolbar

  1. Click the New Sites button ()
    • The New Sites panel opens

Figure 2-2. Define polyisoprene site.

  1. For Name, input PI
  2. For Color, choose green
  3. For Radius, input 8.00
  4. For Mass, input 1000.00
  5. Click OK
    • A green sphere is added to the right-hand column in the Coarse-Grained Sketcher

 

Note: Radius units are Å and mass units are AMU

Figure 2-3. Draw polyisoprene block of chain.

  1. Click and drag in the Sketcher to connect 14 PI sites

Note: Each PI site represents ~10 isoprene monomer units. See Section 5 of the tutorial for details on estimation of mass and radius

Figure 2-4. Add and define polystyrene site.

  1. Click the New Sites button ()
    • The New Sites panel opens
  2. For Name, input PS
  3. For Color, choose orange
  4. For Radius, input 8.00
  5. For Mass, input 1000.00
  6. Click OK
    • An orange sphere is added to the right-hand column in the Coarse-Grained Sketcher

Note: Each PS site represents ~10 styrene monomer units. See Section 5 of tutorial for details on estimation of mass and radius

Figure 2-5. Draw polystyrene block of chain and create project entry.

  1. Click on an end of the polyisoprene chain and drag in the Sketcher to connect 1 PS site
  2. Click and drag in the Sketcher to connect an additional 5 PS sites
    • 6 total PS sites should be present
  3. Next to Title, input PS-PI
  4. Click Create Project Entry
    • PS-PI is added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.
    • PS-PI is includedthe entry is represented in the Workspace, the circle in the In column is blue. the workspacethe 3D display area in the center of the main window, where molecular structures are displayed.
  5. Close the Coarse-Grained Sketcher panel

2.2 Add coarse-grained polymers to unit cell

Figure 2-6. Select coarse-grained molecule.

  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. PS-PI

Figure 2-7. Warning in Disordered Builder.

  1. Go to Tasks > Materials > Structure Builders > Disordered System
    • The Disordered System Builder opens
  2. In the Warning, click OK

 

Note: The force field will be applied at a later step

Figure 2-8. Disordered System Builder set up.

  1. In the Disordered System Builder, for Number of molecules, input 200
  2. Set the Initial State to Tangled chain
  3. Change the Job name to PS-PI_cell
  4. Click Run
    • This job takes ~10 minutes on a local CPU host
    • A banner appears when the job has been incorporated
    • A new group titled PS-PI_amorphous is added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.
  5. Close the Disordered System Builder

Figure 2-9. Select and include the amorphous unit cell.

  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 entry PS-PI_cell_all_components_amorphous

Note: If the unit cell box is not displayed, toggle it on by clicking Unit Cell in the Workspace Configuration Toolbar ()

  1. Click and drag the left mouse button to rotate the structure

Note: See the Custom Mouse Actions Panel help topic for further information on mouse actions

3. Applying a Coarse-Grained Force Field

A repulsive harmonic force field can be applied to the coarse-grained unit created in the previous section. The dissipative particle dynamics technique, commonly used for polymers and other soft matter systems, uses repulsive harmonic potentials. The repulsive harmonic non-bond interaction parameters can be obtained by atomistic simulation or fit of experimental data. The parameters for polystyrene and polyisoprene are supplied. Bond potential terms can be obtained based on relation to known parameters (Guess), an average of bonded atomistic interaction (Average), user input based on supplied information (Edited), or from a database of known parameters (Database). This tutorial will use Guess, Average, and Edited parameters

In this tutorial, the parameters in the force field use real units. Many coarse-grained force fields in the literature, such as those used in the dissipative particle dynamics technique, use reduced units. Ensure that conversions are made to real units prior to input into the force field panel.  Please refer to Section 5 of this tutorial for details on how the forcefield parameters are estimated and converted to real units for this example.

Figure 3-1. Review Site parameters.

  1. With PS-PI_cell_all_components_amorphous selected(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries. and includedthe entry is represented in the Workspace, the circle in the In column is blue., go to Tasks > Materials > Classical Mechanics > Coarse Grain Models > Coarse-Grained Force Field Assignment
  2. In the Site tab, for both sites, leave the Mass set to 1000.00 and the Charge set to 0.00

Figure 3-2. Edit Bond parameters.

  1. Go to the Bond tab
  2. For each Type, leave Req/Å set to 16.00
  3. For each Type, set k/(kcal/mol)/Å2 to 0.02
    • An E is next to the parameter, indicating it is edited

 

 

Note: Hover over the letter next to the parameter to see a tooltip description

Figure 3-3. Edit Potential and Density.

  1. Go to the Nonbond tab
  2. For Potential, choose Repulsive harmonic
  3. Keep Reduced density set to 3
  4. Change Cutoff distance (Å) to 17.5598
    • This will automatically change the density to ~ 0.92.

Figure 3-4. Edit nonbond information.

  1. For Nonbond Type PI,PI, set a/(kcal/mol)/Å2 to 0.0235
  2. For Nonbond Type PI,PS, set a/(kcal/mol)/Å2 to 0.0357
  3. For Nonbond Type PS,PS, set a/(kcal/mol)/Å2 set 0.0235
  4. Next to Force field name, type tutorial

 

Note: If you do not see the bond types table above the Force field name, expand the panel size

Figure 3-5. Run force field assignment.

  1. Retain the default Desmond input file to create name and click Run
    • A banner appears when the new structure has been incorporated
    • A new entry titled PS-PI_cell_all_components_amorphous is added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion. in a new entry group entitled Coarse-Grained Force Field Assignment (1)
  2. Close the Assign Force Field panel

 

Note: Parameters can be saved for future use by clicking Save

 

Note: It is important to close the panel after force field assignment to prevent slow response for subsequent operations

Figure 3-6. Output in the workspace.

Output of the Force Field Assignment procedure

4. Relaxing and Equilibrating Structures

A series of molecular dynamics simulations can be performed on the unit cell of the PS-PI block copolymer.  The forcefield applied in the previous sections includes Repulsive Harmonic potentials, therefore the appropriate relaxation and MD settings will be applied.  The separation of the PS and PI blocks into distinct phases is apparent after the relaxation and equilibration of the structure.

4.1 Run Molecular Dynamics simulation

Figure 4-1. Select Relaxation protocol.

  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 new entry PS-PI_cell_all_components_amorphous
  2. Go to Tasks > Materials > Classical Mechanics > MD Simulations > MD Multistage Workflow
    • The MD Multistage Workflow panel opens
    • The panel can also be conveniently accessed using the Workflow Action Menu button () directly from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.
  3. Check Relaxation protocol
  4. Choose Repulsive harmonic

Figure 4-2. Edit Stage 4 Molecular Dynamics.

  1. In Stage 4, for Stage type, choose DPD Molecular Dynamics
  2. For Simulation time, next to Total, input 3
  3. For Recording interval (ps), next to Trajectory, input 100
    • This will generate 30 frames in the trajectory.
  4. For Ensemble class, choose NVT
  5. For Time step, type 20
    • The time step for dissipative particle dynamics simulations can be many factors larger than all-atom simulations. 20 is chosen for this example as a stable time step for this system
  6. In the MD Multistage Workflow panel, for Job name, type multistage_simulation_PS-PI
  7. Adjust the job settings () as needed
    • This job requires a GPU host.
  8. If you would like to run the job yourself, click Run. Otherwise, go to File > Import Structures, navigate to the provided tutorial files and OpenSection_04 > multistage_simulation_PS-PI > multistage_simulation_PS-PI-out.cms

Note: Available hosts will depend on resources identified during installation of Maestro Materials Science

Figure 4-3. Select and include PI-PS_cell_amorphous. Open the Trajectory Viewer.

  1. A new entry is added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion. titled PS-PI_cell_all_components_amorphous
  2. 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 entry and Double-Click the to view the trajectory
    • The Trajectory Viewer appears

Figure 4-4. Adjust frame to 31.

  1. For Current Frame, input 31
    • The 31st frame of the trajectory is shown in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed.
  2. Click and drag the left mouse button to rotate the structure
  3. Close the Trajectory Viewer using the () button in the top-right corner of the Trajectory Viewer (in the bottom right corner of the workspacethe 3D display area in the center of the main window, where molecular structures are displayed.)

4.2 View polystyrene phase

Figure 4-5. Open Atom Selection panel.

Suppose we want to view only the polystyrene phase:

 

  1. From the main menu, go to Select > Define
    • The Atom Selection panel opens

Figure 4-6. Select PI sites.

  1. In the Atom tab, click Atom name
  2. For Atom name, click PI
  3. Click Add
  4. Click OK
    • The PI sites are now selected

Figure 4-7. Undisplay PI sites.

  1. Open the Style menu at the top of the workspacethe 3D display area in the center of the main window, where molecular structures are displayed.
  2. Click Undisplay selected atoms
    • The PI sites are no longer shown

Figure 4-8. Select PS sites.

  1. Go to Select > Visible
    • The PS sites are selected

Figure 4-9. Open Advanced Surface panel.

  1. Go to Workspace > Surface > Advanced
    • The Advanced Surfaces panel opens

Figure 4-10. Create a surface for PS sites.

  1. For Resolution, choose Low
  2. For Probe radius, input 8
  3. For VDW radius scale, input 4
  4. Click Create
    • Surface is created in < 1 minute
    • A banner appears when the surface has been incorporated
    • An S is added to the PS-PI_amorphous entry

Figure 4-11. Visualizing the surface.

  1. Name the surface what you’d like
  2. Click and drag the left mouse button to rotate the structure

 

Note: A bicontinuous phase can be seen

5. Appendix - Calculating Parameters

The force-field parameters used in this tutorial are based on the dissipative particle dynamics technique and use interaction parameters given in Soto-Figueroa et al.  It is necessary to convert all parameters from non-dimensional units to real units. This section contains reference material describing the specific conversions necessary.

5.1 Experimental and literature parameters

The following parameters are derived from experimental or literature values for polystyrene and polyisoprene:

  • Molecular Weight of polystryene monomer: 104 g/mol
  • Molecular Weight of polyisoprene monomer: 68 g/mol                                                                                                                                                                                                                                                                                   
  • Temperature:  300 K
  • Density of polystryene/polyisoprene block copolymers at 300 K: 0.92 g/cm3
  • Flory-Huggins Chi parameter, PS-PI: 0.3955
  • Repulsive Harmonic Equation: U(r) = A*(r-rc)2

5.2 DPD parameters

The following parameters are standard DPD parameters used in this example:

  • Site density: 3 sites/volume unit
  • Repulsive Harmonic aii: 25
  • Repulsive Harmonic aij: Equation (aii+3.497ij)
    • Note: Equation results in compressibility of water at site density of 3 and  aii of 25
  • Number of monomers per site: approximately 10
  • Molecular weight per site: use molecular weight of polystryene to get 1040 g/mol or approximately 1000 g/mol

5.3 Calculated parameters

The following parameters are calculated:

  • Energy Standard Unit, kBT: 2493 J/mol or 0.596 kcal/mol at 300K
  • Volume per site: 1877 Å3/site
    • Note: calculated from density of copolymers and molecular weight per site
  • Radius per site: 7.6 Å or approximately 8 Å
    • Note: calculated from volume per site and assume spherical site
  • rc (cutoff radius): 17.8 Å
    • Note: calculated as (site density * volume per site)⅓
  • Aii: 0.0235 kcal/mol
    • Note: conversion from DPD parameter using Energy Standard Unit and 2rc2. Factor of 2 is necessary to match DPD standard definitions with Desmond standard potentials.
  • aij: 38
    • Note: calculated from Repulsive Harmonic aij equation
  • Aij: 0.035 kcal/mol
    • Note: conversion from DPD parameter using Energy Standard Unit and 2rc2. Factor of 2 is necessary to match DPD standard definitions with Desmond standard potentials.
  • Bond k: 0.02 kcal/mol
    • Note: set as approximately Aii
  • Bond R: 16 Å
    • Note: set as 0.925*rc which results in the appropriate bond-length distribution

6. Conclusion and References

In this tutorial, we completed a workflow to build two coarse-grained polymer chains and construct a disordered unit cell containing the polymer chains. We generated a blend of polystyrene and polyisoprene. Then a repulsive harmonic (dissipative particle dynamics) force field was applied.  Phase separation was observed through a relaxation and 5 ns molecular dynamics simulation. 

For further learning:

For introductory content, focused on navigating the Schrödinger Materials Science interface, an Introduction to Materials Science Maestro tutorial is available.Please visit the materials science training website for access to 100+ tutorials. For scientific inquiries or technical troubleshooting, submit a ticket to our Technical Support Scientists at help@schrodinger.com.

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

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

For further reading:
  • Dissipative Particle Dynamics Study of Order-Order Phase Transition of BCC, HPC, OBDD, and LAM Structures of the Poly(styrene)-Poly(isoprene) Diblock Copolymer. DOI:10.1021/a7028264

7. 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.

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.