Struggling with Consistency? How to Use Your Own GROMACS Version in SAMSON

Getting consistent results across machines and ensuring reproducibility in molecular simulations is a real challenge. While default software versions bundled with simulation tools are great for convenience, you might have faced cases where:

  • You need to match the exact GROMACS version used in a previous study.
  • You’ve optimized a custom GROMACS build for specific hardware.
  • You simply want to stay on the same version across different environments.

If you’re using SAMSON’s GROMACS Wizard, there’s a handy way to switch to your own GROMACS version for local computations. Let’s walk through how you can do this, and why it’s useful.

Why use a custom GROMACS version?

The version of GROMACS you use can impact your simulation results due to changes in algorithms, bug fixes, or performance-related optimizations. While SAMSON comes with a recent GROMACS version, working with your own version might be essential when:

  • Reproducing results from published work.
  • Aligning your workflow with a specific computational infrastructure.
  • Using extensions or compiled modifications specific to your GROMACS build.

How to switch to a custom GROMACS version in SAMSON

First, open the Settings in the GROMACS Wizard:

Open settings

Check the option Use a different GROMACS version and you’ll be able to provide two key pieces of information:

  1. Path to GROMACS executable:
    You’ll need to locate your compiled GROMACS executable on your system. This is generally called gmx (Linux/Mac) or gmx.exe (Windows). Click the browse button browse to select it. Once selected, SAMSON will try to validate the executable and display its version (or show “invalid” if it can’t recognize it).
  2. Path to force fields:
    You also need to specify the path to the folder containing your GROMACS force fields, typically something like $HOME/gromacs/share/top/.

Custom GROMACS path

Things to keep in mind

  • You can always switch back to the default bundled GROMACS version, which is useful if you’re collaborating with colleagues who don’t use a custom version.
  • Make sure that your local GROMACS version is compiled with the options you expect (e.g., GPU support, MPI) before using it in your simulations.
  • This setup only affects local jobs. Cloud jobs will still use the default settings from SAMSON’s infrastructure.

Conclusion

Being able to use a custom GROMACS version within SAMSON gives you more control and flexibility, helping address key pain points like reproducibility and tailored performance optimizations. If you’ve already installed a specialized GROMACS build on your machine, making SAMSON’s GROMACS Wizard use it is just a few clicks away.

📘 Learn more in the full GROMACS Wizard settings documentation.

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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