How to Use a Custom GROMACS Version in SAMSON’s GROMACS Wizard

If you’re a molecular modeler using GROMACS for your simulations, there’s a high chance you’ve encountered the need to rely on a specific version of GROMACS for reproducibility or to meet the requirements of your workflow. SAMSON’s GROMACS Wizard has you covered by allowing you to use your locally-installed GROMACS version seamlessly. Here’s a step-by-step look at how you can do this!

Why Use a Custom GROMACS Version?

Although the GROMACS Wizard ships with one of the latest versions of GROMACS, researchers may need to use a specific version of the software for several reasons:

  • Reproducibility: Some studies require revisiting past setups, making it mandatory to use the same GROMACS version.
  • Compatibility: Your workflow may include tools or files that were optimized for a specific version of GROMACS.
  • Custom Installations: You may have optimized or tailored GROMACS for your hardware and wish to integrate this into SAMSON.

Getting Started with Your Custom Version

To link your locally-installed GROMACS version to the GROMACS Wizard, follow these steps:

  1. Open the GROMACS Wizard Settings: Start by clicking on the Settings button at the top of the GROMACS Wizard interface.
  2. Enable the Option to Use a Custom GROMACS: In the settings menu, check the box labeled Use a different GROMACS version.
  3. Provide the Required Paths: You’ll need to provide two paths:
    1. A path to the GROMACS executable: On Windows, this will typically be a gmx.exe file, while on Linux and macOS, it’s simply gmx. Use the browse button to browse and select the file. If the selected executable is valid, the GROMACS version will be displayed.
    2. A path to the force fields folder where all the forcefield.ff directories are stored. For instance, on Linux or macOS, this is often located at $HOME/gromacs/share/top/.

Below is an illustration of how the settings interface appears when linking a custom GROMACS installation:

Custom GROMACS path

Take Advantage of Versatility

By integrating your own version of GROMACS into SAMSON’s GROMACS Wizard, you gain the freedom to harness your preferred software environment while still benefiting from the user-friendly interface and computational power of SAMSON. Whether for testing specific force fields, ensuring reproducibility, or conducting advanced studies, this flexibility can significantly enhance your modeling workflows.

Learn More

Interested in exploring more of GROMACS Wizard’s features? You can dive deeper into the original documentation at this link.

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

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