Still Using the Wrong GROMACS Version?

If you’re working with GROMACS for molecular dynamics simulations, there’s a good chance you’ve encountered compatibility issues between versions. Whether you’re trying to reproduce published results, align with your lab’s computing environment, or troubleshoot strange errors, using a specific version of GROMACS can be crucial.

This is where the GROMACS Wizard in SAMSON comes in handy. While it comes bundled with a recent and curated GROMACS version ready to use, it also offers a simple way to switch to the version you really need—without configuring complex environment variables or altering your system path.

Why would you want to use a custom GROMACS version?

  • Reproducibility: Use the same version as a published study to ensure consistency.
  • System compatibility: Match your institution’s cluster environment or another pre-installed setup.
  • Feature-specific needs: Leverage certain features or fixes available only in a particular version.

How to switch GROMACS versions easily in GROMACS Wizard

First, open the GROMACS Wizard in SAMSON and click on the Settings icon located at the top interface:

Open settings

Next, check the option Use a different GROMACS version. You’ll be prompted to provide two essential pieces of information:

  1. Path to the GROMACS executable: This is usually gmx on Linux/macOS or gmx.exe on Windows. You can use the file browser to navigate and select it. If valid, the version will be displayed; if not, you’ll see “invalid.”
  2. Path to your force fields: Specifically, where the .ff folders such as amber99sb.ff or gromos53a6.ff reside. On Linux/macOS, this might be something like $HOME/gromacs/share/top/.

Custom GROMACS path

Once done, GROMACS Wizard will use your specified version for local computations. No permanent changes to your environment are necessary, making this an especially useful feature if you’re collaborating across multiple machines or users.

Good to know

  • You can always revert back to the bundled version by unchecking the option.
  • This configuration only affects local jobs run on your machine, not those submitted to the cloud.
  • If you frequently switch environments, this makes temporary configuration changes safe and reversible.

Whether you’re a molecular modeler needing platform consistency, or a student trying to align your setup with a published tutorial, this feature can save both time and frustration. Plus, it’s integrated right into SAMSON, so you don’t need to manage separate installations.

For complete details, visit the original documentation page: GROMACS Wizard Settings – SAMSON Documentation

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.

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