If you use GROMACS frequently for molecular dynamics simulations, you’re probably familiar with situations where you need to run simulations with a specific version of GROMACS — for example, for reproducibility in publications, for performance comparisons, or simply because your tools or workflows depend on it.
By default, the GROMACS Wizard Extension in SAMSON ships with one of the latest versions of GROMACS. This gives most users an optimized and ready-to-run setup for production simulations. But what if you want to use your own GROMACS installation?
Fortunately, SAMSON makes it easy to plug in your own version of GROMACS. Let’s walk through how and why you might want to use this option.
Why switch to a custom GROMACS version?
- Reproducibility: If a previous project used an earlier version of GROMACS, you might want to ensure consistency by reusing the same version.
- System-specific optimization: You may have built a custom GROMACS with compiler flags optimized for your hardware.
- Compatibility with tools: Some force fields and tools may depend on features only available in specific versions.
How to switch GROMACS versions in SAMSON
Begin by opening the GROMACS Wizard and clicking on the Settings button at the top:
In the settings panel, check the option Use a different GROMACS version. This will prompt you to provide two paths:
- GROMACS executable path: This is the path to
gmxorgmx.exe, depending on your OS. SAMSON will automatically validate the executable and display its version (or indicate if it’s invalid). - Force fields path: This should point to the folder containing force field directories (e.g.,
$HOME/gromacs/share/top/on Linux/macOS).
Tips for success
- Ensure that your custom GROMACS was compiled with the compatible options for your operating system and architecture.
- If you run into errors using a different GROMACS version, double-check the executable permissions and library dependencies.
- Remember that using a validated binary version helps prevent compatibility issues — only switch when you’re sure of your setup’s requirements.
This simple ability to switch versions in the GROMACS Wizard can save time and give you a much-needed level of flexibility for more advanced simulation workflows. It’s especially important if reproducibility and customization are part of your workflow.
Want to go further? Check out the full documentation section on settings and customization options here: https://documentation.samson-connect.net/tutorials/gromacs-wizard/settings/.
SAMSON and all SAMSON Extensions are free for non-commercial use. To download SAMSON and start exploring, visit https://www.samson-connect.net.