A Practical Guide to Preparing Coarse-Grained Systems with GROMACS Wizard

For molecular modelers, preparing a coarse-grained (CG) system can be a crucial yet complex task. Whether you’re working on simulating proteins or larger molecular assemblies, the process involves multiple steps—from setting up a periodic box to solvating the system and neutralizing charges. In this guide, we delve into how the GROMACS Wizard, an extension within the SAMSON platform, simplifies this process for CG systems under the MARTINI v.3.0.0 force field.

Why System Preparation Is Critical

Preparation is the foundation of molecular dynamics (MD) simulations. A misstep here—such as insufficient solvation, inaccurate box sizes, or unbalanced charges—can lead to erroneous dynamics or failed simulations. For those using MARTINI force fields, ensuring compatibility between system inputs and the force field parameters is especially important, and this is where GROMACS Wizard excels.

Step-by-Step Guide to Preparing a CG System

Here’s how to prepare a CG system using GROMACS Wizard:

  1. Set Up the System: Under the Prepare tab, choose the Set system option and switch the input to Folder. Browse and select the folder containing your CG structure and topology files (e.g., *_CG.pdb and *_CG.top files).

    Set system from system folder

  2. Load the PDB File: Once your input folder is selected, click Load next to the detected PDB file. This action computes the periodic box for the system and loads it into a new document within the GROMACS Wizard.

    Computed periodic box

  3. Verify Force Field Settings: If your CG system is based on MARTINI 3.0.0 (such as one generated via Martinize2), the Wizard automatically applies the appropriate force field and solvent model. Double-check that the solvent is set to Martini water and the force field is martini_v.3.0.0.

    Choose MARTINI v.3.0.0 force field

  4. Add Solvent: If solvation is required for your system, use the Add solvent option. Configure the solvent parameters via the gear icon. To avoid atomic clashes, increase the default van der Waals distance from 0.105 nm to a higher value such as 0.21 nm, which better suits CG bead models where each represents multiple water molecules.

    Open solvent options

    Solvent options

  5. Neutralize the System: To ensure the system’s electrical neutrality, select ions to be added, either to neutralize the system or introduce a specific salt concentration. Remember, ions are added by replacing solvent molecules, so solvation must be enabled before this step.

    Add ions - Salt concentration

  6. Finalize Preparation: Click Prepare to complete the setup. The Wizard generates all necessary files and settings for your MD simulation. You can inspect the prepared system, reload it for visualization, or proceed to the next steps, including minimization and equilibration.

    Prepared CG system

Final Thoughts

The GROMACS Wizard within SAMSON streamlines a task that otherwise requires juggling multiple tools and scripts. By automating many decisions, such as force field compatibility and solvent addition, it reduces the possibility of human error while saving time. To explore detailed steps and additional customization tips, visit the official documentation.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at SAMSON Connect.

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