When You Need That Specific GROMACS Version

Reproducing published results or running benchmarks that match exactly what others have done is a common challenge in molecular modeling. One subtle but impactful issue? GROMACS version mismatches. Even minor updates to GROMACS can introduce changes in default settings, force field interpretations, or numeric handling that ripple through to your final results. That’s why many researchers try to stick with one specific GROMACS version across their workflows.

Fortunately, the GROMACS Wizard in SAMSON offers an easy way to use a custom, locally installed GROMACS version. So if your cluster is set up with GROMACS 2021.3 and that’s what your collaborators are using, you’re in luck. You don’t have to change a thing—you can keep using that version in the SAMSON interface.

How to Set Up a Custom GROMACS Version

To use a different version of GROMACS in the GROMACS Wizard, open the Wizard and click the Settings button at the top:

Open settings

Under the settings window, check the option labeled Use a different GROMACS version. You’ll then need to provide two specific paths:

  1. Path to the GROMACS executable — This is typically gmx or gmx.exe. Click the browse button (browse) and select your GROMACS binary. Once selected, the wizard displays the detected version (or notifies you if the executable is invalid).
  2. Path to the force fields — This is usually something like $HOME/gromacs/share/top/ on Linux/macOS or the corresponding directory on Windows. It contains folders like amber99sb-ildn.ff used during preprocessing.

Custom GROMACS path

Why This Matters

If your systems or protocols depend on a specific GROMACS behavior, enabling your custom version in SAMSON ensures consistency. For example:

  • Reproducing simulations published with older GROMACS versions
  • Checking results across versions to test numerical sensitivity
  • Running custom builds with uncommon compile flags or experimental patches

This feature helps bridge the command-line flexibility of GROMACS with the visual, interactive environment of SAMSON, and removes the friction of switching between GUI and terminal while ensuring precision.

You can always switch back to the default shipped GROMACS version by unchecking the option and resuming regular use — useful when running standard systems or cloud jobs.

To learn more and access full documentation, visit the GROMACS Wizard settings guide.

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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