Step-by-Step Guide to Preparing Coarse-Grained Systems with GROMACS Wizard

For molecular modelers looking to dive into coarse-grained simulations, preparing your system correctly is a vital first step. Yet, the process of assembling topology files, setting up periodic boxes, solvating the system, and adding ions can seem daunting. Thankfully, the GROMACS Wizard in the SAMSON platform is here to simplify and streamline this workflow.

Why Preparation Matters

A coarse-grained (CG) system reduces molecular complexity while retaining key interactions, making it an efficient tool for large-scale simulations. However, improper preparation can lead to unstable simulations or inaccurate results. In this blog post, we’ll walk through a structured and user-friendly approach to preparing a CG system using the GROMACS Wizard. Let’s start!

Getting Started: Key Inputs

Before jumping into GROMACS Wizard, you’ll need a valid CG model. If you’ve created your model using Martinize2, ensure the generated topology (.top) and structure (.pdb) files are organized in a single folder. This preparation will make your workflow smoother.

Step-by-Step: Preparing Your CG System

Here’s how you can easily prepare your system:

  1. Open the GROMACS Wizard and navigate to the Prepare tab: This is your starting point for setting up the system.
  2. Load your input files: Switch the From dropdown to Folder and choose the folder containing your topology and structure files. Simply click Browse… and select the appropriate directory. Once loaded successfully, the wizard will detect PDB, TOP, and ITP files as shown below:

    List of input files

  3. Choose a force field: If your system was modeled using Martinize2, the GROMACS Wizard will automatically set the force field to martini_v.3.0.0. If needed, adjust the force field manually, especially if you’re including custom force fields. Here’s how the interface looks for MARTINI force fields:

    Choose MARTINI v.3.0.0 force field

  4. Set up the periodic box: Load your PDB file by clicking the Load button. This step computes the periodic box necessary for your simulation. You can modify the box size or switch the cell type to Rhombic dodecahedron for efficiency. An example periodic box setup looks like this:

    Computed periodic box

  5. Add solvent: Check the Add solvent option and click the gear icon for detailed settings. Increase the default van der Waals distance (e.g., to 0.21 nm) to prevent close-packing of coarse-grained beads that might cause simulation errors. This adjustment ensures proper solvent density. Here’s the configuration screen:

    Solvent options

  6. Neutralize and add ions: The wizard supports easy neutralization and salt concentration adjustments. Choose positive and negative ions, which will be added by replacing solvent molecules. If you want to add more ions or simulate specific saline environments, the interface supports customization:

    Add ions - Salt concentration

  7. Finalize preparation: Click Prepare to process the configuration. You can now inspect the system or move forward to simulation steps like minimization and equilibration. Below is an example of a prepared coarse-grained system:

    Prepared CG system

Next Steps

Once the preparation phase is complete, your system is ready for energy minimization, equilibration, and production molecular dynamics (MD) simulations. Each of these steps plays a critical role in ensuring the stability and accuracy of your simulations.

If you’d like deeper insights into using the GROMACS Wizard, check out the original documentation here.

*Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get started today by downloading the platform at SAMSON Connect.

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