Setting Up Custom GROMACS Versions for Molecular Dynamics

For molecular modelers aiming to ensure reproducibility or tap into the specific features of a particular GROMACS version, the ability to customize your GROMACS setup can be pivotal. SAMSON’s GROMACS Wizard simplifies the process of integrating a custom GROMACS installation into your workflow, offering flexibility and control for local molecular dynamics simulations.

Why customize your GROMACS version?

Though GROMACS Wizard comes with one of the latest versions of GROMACS packaged for convenience, you might find yourself needing a different version to ensure reproducibility, use system-specific builds, or access deprecated features. Fortunately, the GROMACS Wizard makes it easy to configure and switch to your locally installed version of GROMACS.

Steps to Set Up a Custom Version

First, open the GROMACS Wizard and locate the Settings button at the top of the interface:

Open settings

Follow the steps below to configure your custom setup:

  1. Enable the custom version option: In the Settings menu, check the option titled “Use a different GROMACS version”.
  2. Provide paths: Specify the following paths:
    • Path to the GROMACS executable: For example, gmx.exe on Windows or gmx on Linux/macOS. Use the browse button to browse for the file.
    • Path to the force fields folder: Identify the directory where the forcefield.ff folders are stored. On Linux/macOS, this might look like $HOME/gromacs/share/top/.

Custom GROMACS path

The Settings panel will validate your selected paths. If the GROMACS executable is recognized, its version will be displayed. Otherwise, you’ll see an “invalid” message, prompting you to recheck the provided path.

Tips for Reproducibility

If ensuring reproducibility is a priority, it’s recommended that you decide in advance which exact GROMACS release and force-field directory you want to use. By choosing the same settings every time, you avoid discrepancies and can ensure consistency across simulations.

Keep in mind that the custom settings you configure here apply exclusively to local computations. For workflows requiring cloud-based processing, local performance parameters or custom versions will not be considered.

Next Steps

Once your custom GROMACS version is set up, return to the computation you want to run in GROMACS Wizard and launch it with the selected paths and performance configurations. This flexibility ensures your simulations are both efficient and tailored to your needs.

For more detailed guidance, visit the official documentation page at GROMACS Wizard – Settings.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get started today at SAMSON Connect.

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