Switching to Your Own GROMACS Version in SAMSON: When and How

If you’re working with molecular dynamics simulations, chances are you’ve used GROMACS, a powerful and widely used MD engine. SAMSON’s GROMACS Wizard makes it easy to run GROMACS computations, both locally and in the cloud. But what if you need to run your simulation with a specific version of GROMACS—one installed on your own system?

This is a common need for molecular modelers who want to ensure reproducibility, test new features in a development build, or maintain compatibility with older workflows. Fortunately, SAMSON’s GROMACS Wizard provides a simple way to use your own GROMACS installation.

Why use a custom GROMACS version?

Depending on your needs, using a custom version of GROMACS might be essential. Some possible scenarios:

  • You’ve added patches or custom code to GROMACS for specialized force fields or analysis tools.
  • You need to replicate published simulation results that used a particular GROMACS version.
  • Your IT department provides centrally managed builds with optimized performance on your cluster.

In all these cases, being locked to a prebuilt version can be limiting. SAMSON acknowledges this flexibility need by allowing users to configure their own GROMACS paths right from the GROMACS Wizard interface.

Setting up your local GROMACS

To get started, open the GROMACS Wizard in SAMSON and click the Settings button at the top:

Open settings

Inside the settings panel, check the option “Use a different GROMACS version”. You’ll be prompted to specify two critical paths:

  1. Path to the GROMACS executable: This is typically gmx on Linux/MacOS or gmx.exe on Windows. Browse to the exact location of this binary using the browse button. SAMSON will check the validity and display the executable’s version.
  2. Path to force fields: This directory should contain your GROMACS forcefield folders (e.g., amber99sb.ff, charmm27.ff). A typical location on Linux might be $HOME/gromacs/share/top/. Make sure the folder exists and is populated with the necessary files.

Once both paths are filled in correctly, your local GROMACS version will be used for all your local simulation jobs!

Custom GROMACS path

Things to keep in mind

  • If SAMSON displays “invalid” next to your GROMACS executable, double-check that the path is correct and that the executable has permission to run.
  • Be sure that your force field folder is complete; missing files may cause your simulation setup to fail.
  • The selected custom paths apply only to local simulation jobs. Cloud jobs will still run with SAMSON’s default GROMACS version.

Final thoughts

This feature empowers SAMSON users with more control over their GROMACS environments, supporting reproducible science and custom workflows without requiring command-line gymnastics. Whether you’re juggling several GROMACS builds or simply want to use the version your team standardized on, the GROMACS Wizard makes switching straightforward and visual.

To learn more about customizing GROMACS in SAMSON, visit the full documentation: https://documentation.samson-connect.net/tutorials/gromacs-wizard/settings/

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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