Switching GROMACS Versions Without Breaking a Sweat

Many molecular modelers rely on GROMACS for running molecular dynamics simulations. It’s fast, robust, and widely used. However, there’s one issue that pops up often: how to use your specific version of GROMACS from within another platform or software like SAMSON?

This is especially relevant if you’re trying to replicate past experiments using a specific version of GROMACS, or if your lab infrastructure already has a fine-tuned GROMACS setup. Good news: GROMACS Wizard in SAMSON provides a simple and flexible way to use a custom GROMACS version locally.

Why you might want to choose your own GROMACS version

Heavy GROMACS users know that small changes in versions can lead to subtle (or not so subtle) differences in outcomes. Software updates often bring changes to force fields, command flags, or file formats.

The copy of GROMACS shipped with GROMACS Wizard is near the latest, but that’s not always ideal. You may want your system to use a version installed by your sysadmin, or one you compiled yourself for optimal performance on specific hardware.

Configuring your own GROMACS version in GROMACS Wizard

Thankfully, switching to your version of GROMACS in the GROMACS Wizard requires only a few steps:

1. Open the GROMACS Wizard in SAMSON and click on the Settings button at the top.

Open settings

2. In the Settings window, enable the option Use a different GROMACS version.

3. Provide two paths:

  • The path to the gmx executable (gmx.exe on Windows, or gmx on Linux/macOS). Use the browse button to select it.
  • The path to your GROMACS force field folder (e.g., $HOME/gromacs/share/top/ on Linux/macOS).

If a valid executable is detected, its version will be displayed. If something goes wrong, you’ll see an invalid status instead. This helps in verifying everything is correctly linked before moving forward.

Custom GROMACS path

When and where this matters most

Switching versions is especially handy in cases like:

  • Trying to match simulation results from literature based on an older GROMACS version.
  • Running a validated GROMACS version from your HPC cluster on your local machine.
  • Quick troubleshooting when an error only appears in one version of the software.

Things to keep in mind

This configuration will only affect local computations. If you’re running jobs on the cloud through SAMSON, it will still use the default environment provided by the platform. So choose accordingly depending on where your simulations run.

Using a custom GROMACS setup in SAMSON lets you bring an already optimized workflow into an integrated design environment—no need to abandon one for the other.

For detailed instructions and further options around performance tuning, warnings management, and more, visit the official GROMACS Wizard documentation page: https://documentation.samson-connect.net/tutorials/gromacs-wizard/settings/

SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.

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