Preparing Coarse-Grained Systems with GROMACS Wizard

Molecular modelers working with coarse-grained (CG) systems often face challenges when setting up their simulations. Building a proper periodic box, solvating it correctly, and neutralizing the system with ions can be time-consuming and prone to errors. SAMSON’s GROMACS Wizard simplifies this process significantly, providing an intuitive pathway for preparing MD simulations. Here’s how you can save time and effort while ensuring precision.

The Preparation Workflow

The GROMACS Wizard streamlines the preparation of CG systems. Follow these steps to prepare a solvated, periodic MD-ready box:

  1. Head to the Prepare tab in GROMACS Wizard.
  2. Under the Set system section, switch the input source From to Folder. Use the Browse… button to select a folder containing the required input files (.pdb and .top). These files should represent your CG model. For instance, if you’ve created your model using the Martinize2 SAMSON Extension, you’ll need to use the folder containing the *_CG.pdb and *_CG.top files.

    Set system from system folder

  3. Once the files are detected by GROMACS Wizard, load the primary PDB file by clicking the Load button. This step imports the system into a new document and computes a periodic box for it automatically.
    Computed periodic box
  4. If the CG model is derived from Martinize2, the force field will automatically be set to MARTINI v.3.0.0, with the default Martini water configured as the solvent. Ensure that these settings are correct before proceeding.

    Choose MARTINI v.3.0.0 force field

  5. To solvate the system, enable the Add solvent options. Clicking the gear icon (Add solvent options) allows you to fine-tune parameters such as van der Waals distances. For CG models, it’s recommended to increase this parameter to 0.21 nm to avoid clashes.

    Solvent options

  6. If needed, adjust the periodic box size. For example, ensure the solute-box distance is at least 1 nm to prevent overlap with image molecules. Consider using a Rhombic dodecahedron shape, a compact and efficient unit cell geometry.
  7. Add ions to the solvent to neutralize the system or achieve a target salt concentration. Positive and negative ions will replace solvent molecules to meet the specified parameters.

    Add ions - Salt concentration

  8. Click on Prepare. This will finalize the preparation of your box, creating an optimized starting point for energy minimization, equilibration, and production MD.

Prepared CG system

Why This Workflow Matters

Without proper parameter adjustments, issues like molecule overlap or inadequate solvation density can compromise simulations. By following the streamlined steps outlined in SAMSON’s GROMACS Wizard, you not only ensure accuracy but also significantly reduce preparation time. If you’re using custom CG models or solvents, the Wizard also supports advanced options, making it adaptable to varied research scenarios.

Once your system is prepared, you can move directly to minimization, where the auto-fill feature simplifies the transition to simulation phases. For a deeper dive into these workflows or tips on managing specific steps, consult the full documentation.

To explore this tutorial in more detail, visit the full documentation page.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at samson-connect.net.

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