Want to Use Your Own GROMACS Build? Here’s How to Do It in SAMSON

For molecular modelers working with GROMACS, reproducibility and performance can sometimes be at odds. Perhaps you’ve validated a workflow using a specific GROMACS build, or maybe you’ve fine-tuned your installation with particular optimizations for your hardware. But what happens when you’re using an integrative platform like SAMSON’s GROMACS Wizard that ships with its own GROMACS version?

Good news: SAMSON’s GROMACS Wizard lets you override the default GROMACS version and use your own installation instead. This means you can match your simulation environment to previous studies, ensure consistency across systems, or just squeeze out better performance from a build optimized for your machine. Let’s walk through how to make that switch.

Why Use a Custom GROMACS?

  • Reproducibility: Ensuring your version matches previously published work.
  • Performance: Optimized builds can take advantage of newer hardware, compilers, or specific configurations like SIMD instructions or GPU offloading.
  • Advanced Features: Access capabilities in development or special-purpose forks of GROMACS.

How to Set Up a Custom Version in SAMSON’s GROMACS Wizard

Start by opening the GROMACS Wizard in SAMSON and clicking the Settings icon in the upper toolbar:

Open settings

In the Settings pane, enable the option labeled Use a different GROMACS version. You’ll then be asked to supply two paths:

  1. Executable location: This is the path to the gmx binary (gmx.exe on Windows). Use the browse button to locate it. Once selected, SAMSON will verify and display the GROMACS version found.
  2. Force fields folder: Locate the directory containing your forcefield.ff folders — typically something like $HOME/gromacs/share/top/ on Unix-based systems.

Custom GROMACS path

Once configured, all local GROMACS computations in SAMSON will use your selected version — while cloud computations will still use the platform’s built-in version to maintain compatibility on distributed infrastructure.

Things to Keep in Mind

  • Make sure your custom GROMACS installation is compiled and accessible in your system’s environment.
  • The GUI validation helps avoid silent errors — if it says “invalid,” double-check the path and permissions.
  • This configuration only affects local computations, not those run on the cloud via SAMSON.

Final Thoughts

If you’re working on reproducible research, optimizing simulations for your hardware, or simply prefer managing your own versions, SAMSON’s flexibility makes this possible without needing terminal-based scripting.

To learn more, visit the official documentation page here: https://documentation.samson-connect.net/tutorials/gromacs-wizard/settings/

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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