Simplify Molecular Simulations with a Custom GROMACS Setup in SAMSON

For molecular modelers, ensuring reproducibility or utilizing a specific version of a trusted toolkit like GROMACS can be a significant challenge. What if you could easily integrate your custom GROMACS installation into your workflow without juggling between platforms or setups? With SAMSON’s GROMACS Wizard, you can! Here’s how you can leverage this practical feature to boost your performance and precision.

Why Use a Custom GROMACS Version?

By default, the GROMACS Wizard ships with one of the latest versions of GROMACS, perfect for most simulations. However, there are times when you might prefer using your own version of GROMACS:

  • Reproducibility: Certain research requires repeating simulations with an exact software version.
  • System-specific Installation: You might already have a GROMACS version optimized for your local machine or cluster.
  • Legacy Compatibility: Older projects may depend on features or workflows from earlier GROMACS releases.

With SAMSON’s GROMACS Wizard, switching to your custom GROMACS version is straightforward and minimizes disruption to your workflow.

Setting Up a Custom GROMACS Version

To configure your custom version, follow these simple steps:

  1. Click on the Settings button at the top of the GROMACS Wizard interface. You’ll find an intuitive panel where you can adjust your configuration.

    2. Open settings

  2. Select the Use a different GROMACS version checkbox and specify two paths:
    1. Path to the GROMACS executable: Use the browse button to locate your gmx.exe on Windows or gmx on Linux/macOS. The wizard will automatically display the version of your selected GROMACS package (or show “invalid” if it doesn’t recognize the executable).
    2. Path to the Force Fields folder: Point it to the directory containing forcefield.ff folders (e.g., $HOME/gromacs/share/top/ on Linux/macOS).

      Custom GROMACS path

Additional Benefits of Seamless Integration

Once your custom GROMACS version is integrated, you can execute local simulations with full control, ensuring that your computational environment is consistent with your specific needs. For example, you might run calculations to verify results from past projects, test hypotheses under previous configurations, or even benchmark specific versions for performance comparisons.

Additionally, this feature ensures simplicity—no more switching back and forth between external installations and platforms. With SAMSON’s intuitive interface, all your simulations are in one place.

Ready to Start?

Configuring your custom GROMACS installation in SAMSON is a small setup effort that delivers immense flexibility and precision, especially when reproducibility and system compatibility are critical for your work.

To dive deeper, visit the original documentation page for further details.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at this link.

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