One common frustration in molecular modeling workflows is ensuring that simulations are reproducible and compatible with local computing environments. Especially for researchers fine-tuning their systems or working in highly specialized setups, using a customized version of GROMACS instead of the default one can be essential.
Fortunately, SAMSON’s GROMACS Wizard makes this process smoother than you might expect. Here's a walkthrough of how to use your own GROMACS version directly within SAMSON for local computations—and why that might matter to your workflow.
Why use a custom GROMACS installation?
🔹 Reproducibility: You might need to rerun older projects that were performed with specific versions of GROMACS.
🔹 Pre-installed environments: You may already have an optimized GROMACS build installed and configured on your high-performance computing (HPC) system.
🔹 Advanced use cases: You want features, patch sets, or file compatibility that are only available in certain versions.
How to switch to your custom GROMACS version in SAMSON
To begin, open the GROMACS Wizard in SAMSON and click on the Settings button at the top of the interface.
Look for the Use a different GROMACS version checkbox. Once this option is selected, you need to provide two paths:
- Path to the GROMACS executable.
This would typically be something likegmxon Linux/macOS orgmx.exeon Windows. Click the
button to locate it. If the executable is recognized, its version will automatically be shown. If not, “invalid” will appear. - Path to the force fields directory.
This is where GROMACS looks for predefined force fields (*.fffolders). On Linux/macOS, this is usually inside something like$HOME/gromacs/share/top/.
After entering these paths, SAMSON will use your specified version of GROMACS for all local jobs—while still keeping its built-in version available as a fallback or in the cloud.
A tip to keep in mind 🧠
If you frequently switch between different projects requiring different GROMACS setups, consider keeping profiles or notes with the corresponding binary and force field paths. This makes transitioning between them more manageable over time.
What about the cloud?
While your local version is used for computations on your machine, cloud-based jobs still run using the version provided by SAMSON. This can be helpful when consistency isn’t critical or you need offloaded resources.
For more information on GROMACS Wizard settings, including performance tuning and warning overrides, visit the original documentation page: GROMACS Wizard Settings.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.