Streamline Coarse-Grained System Preparation in GROMACS Wizard

Prepping a molecular system for coarse-grained simulations can be a daunting task, especially when balancing accuracy with efficiency. If you’ve been struggling to create periodic boxes, solvate systems, and add ions with the right settings, the GROMACS Wizard in SAMSON offers a guided and intuitive workflow to ease your pain. Here’s how you can prepare a robust coarse-grained (CG) system for simulations, step by step.

Why Proper System Preparation Matters

Accurate molecular dynamics (MD) simulations rely on well-prepared molecular systems. Minor oversights in defining periodic boxes, choosing solvents, or handling force fields can lead to simulation errors or skewed results. With the GROMACS Wizard in SAMSON, these processes are streamlined, helping you focus on your research instead of troubleshooting setup issues.

Essential Steps to Prepare Your Coarse-Grained System

The following concise guide walks you through critical steps of preparing a coarse-grained system in the GROMACS Wizard. In this example, a soluble protein and a MARTINI v.3.0.0 force field setup are used, but the same principles apply to other coarse-grained setups:

  1. Navigate to the Prepare Tab: Open the GROMACS Wizard and begin by selecting the “Prepare” tab for system preparation.

  2. Load Your CG Model: Switch the “From” option to “Folder” under the “Set system” settings. Use the “Browse…” button to locate a folder containing your structure (.pdb) and topology (.top) files.

    Pro Tip: If you’ve already used the Martinize2 SAMSON Extension, select the output folder containing files such as *_CG.pdb and *_CG.top.

    Set system from system folder

  3. Validate Input Files: Once the folder is selected, verify the detected PDB, TOP, and ITP files in the interface. These files will be used for building the simulation system.

    List of input files

  4. Compute the Periodic Box: Load the selected PDB file by clicking the “Load” button. This enables the system to compute a periodic box automatically. A visual representation of the box will allow you to adjust its size and verify correctness.

    Computed periodic box

  5. Choose the Right Force Field: If the CG system originated from Martinize2 for the MARTINI v.3.0.0 force field, the GROMACS Wizard automatically sets it up for you. Double-check the settings to ensure they include the Martini solvent model.

    Choose MARTINI v.3.0.0 force field

    Note: If another CG force field is needed, include it manually. Consult the documentation on using a custom force field.

  6. Solvate Your System: Enable the “Add solvent” option to hydrate the system. Increase the default van der Waals distance to 0.21 nm to avoid overlaps in the solvent spacing.

    Solvent options

    Pro Tip: For custom solvent models, refer to this guide.

  7. Add Ions: Neutralize your system by adding ions, or set a specific salt concentration to mimic physiological conditions. Remember, ions are added by replacing solvent molecules, so ensure the “Add solvent” option is enabled.

    Add ions - Salt concentration

  8. Finalize Preparation: Once all settings are confirmed, click “Prepare” to complete the process. The prepared structure can then be examined or directly used for simulation steps such as minimization and production MD.

Ready to Begin?

Armed with these steps, you can now confidently prepare a reliable coarse-grained system in SAMSON, reducing the time spent configuring parameters manually. To delve deeper into each functionality and explore additional options, check out the full documentation at this link.

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

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