A Clear Roadmap to Preparing Coarse-Grained Systems in GROMACS Wizard

For molecular modelers tackling complex simulations, preparing coarse-grained (CG) systems can feel like navigating a maze. Whether you’re handling large biomolecules or experimenting with customized solvent models, the need for clear, efficient preparation workflows is critical. Fortunately, the GROMACS Wizard in SAMSON offers a streamlined process for preparing CG systems, and today we’ll show you how to make it work for you.

The Challenge: Streamlining CG System Preparation

When working on CG systems, efficiently preparing models—like creating periodic boxes, solvating systems, and adding ions—can save a lot of effort downstream. In a typical workflow, details such as van der Waals distances, solvation densities, and neutralization parameters can derail your progress unless handled correctly. The GROMACS Wizard addresses this pain by offering a dedicated sequence of steps that remove guesswork, limit errors, and provide flexibility in force fields and solvent models.

Step-by-Step Guide to Setting Up a Coarse-Grained System

Here is how to prepare a CG system in the GROMACS Wizard:

  1. Switch to Folder-Based Inputs: Navigate to the Prepare tab and set From to Folder. This lets you organize input files such as structure (.pdb) and topology (.top) files seamlessly.
  2. Use Outputs From Martinize2: For MARTINI 3.0.0 force fields, choose a folder containing *_CG.pdb and *_CG.top outputs from the Martinize2 extension. The wizard will auto-detect these input files, ensuring smooth transitions to the next steps.
  3. Load the System and Configure Periodic Box: Once files are selected, click Load beside the detected PDB file. The wizard automatically computes a periodic box for the system. Adjust the box size (e.g., solute-box distance) to maintain a minimum distance of at least 1 nm between images. You can also switch to space-efficient unit cell types like Rhombic dodecahedron.

    4. Computed periodic box

  4. Select Force Field and Solvent Model: If your CG model is from Martinize2, the wizard will automatically set MARTINI v.3.0.0 for the force field and predefined Martini water as the solvent model. This ensures compatibility for solvation and ion inclusion.

    If you’re using custom CG force fields or solvent models, you can provide them in the system setup. Learn more in the custom force field section.

  5. Solvate the System: Check the Add solvent option and increase the van der Waals distance to around 0.21 nm. With Martini CG beads, the default value of 0.105 nm may cause overlaps due to Martini water beads representing 4 water molecules.
    Solvent options
  6. Neutralize and Add Ions: To neutralize the system or set specific ion concentrations, replace solvent molecules with ions. Positive and negative ions can be customized as per experimental needs.

    Solvent must be added first before ions are added, as ions replace solvent positions during the process.

  7. Finalize Preparation: Hit Prepare. After completing this step, you can inspect the structure in a new document or proceed to the minimization and equilibration steps.

Prepared CG system

Tangible Results and Efficiency

The GROMACS Wizard in SAMSON ensures you move seamlessly from CG model creation—using tools like Martinize2—to system preparation, minimizing potential disruptions. By combining force field validations, adjustable van der Waals settings, and auto-detection of files, the wizard reduces common pain points like solvent clashes or insufficient solute-box distances. These efficiencies make it easier to focus on the science rather than the preparation workflows.

For further details and advanced workflows, visit the comprehensive GROMACS Wizard – Coarse-Grained Systems documentation page.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get started with SAMSON today at https://www.samson-connect.net.

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