Simplify Your Workflow: Using a Custom GROMACS Version in SAMSON

As a molecular modeler, you may find yourself needing precise control over the tools you use. Perhaps the default GROMACS version doesn’t meet your specific project needs, or you require a particular setup for improved reproducibility. Here’s some good news: SAMSON’s GROMACS Wizard allows you to integrate a custom GROMACS version seamlessly for local computations.

Why Use a Custom GROMACS Version?

There are scenarios when switching to a custom GROMACS installation becomes essential. For instance:

  • You have a specific GROMACS version installed on your system that is tailored to your research needs.
  • The default GROMACS package doesn’t support the particular force field or functionality you require.
  • Establishing reproducibility in your simulations is critical, as version differences might lead to unexpected results.

With SAMSON, this process is as straightforward as possible.

How to Switch to a Custom GROMACS

Let’s go step-by-step on how you can configure GROMACS Wizard to use a specific GROMACS version for local computations:

  1. Access the Settings: Launch the GROMACS Wizard in SAMSON and click on the Settings button at the top of the interface.

    2. Open settings

  2. Enable Custom Version: In the Settings panel, check the option Use a different GROMACS version. This unlocks the ability to provide paths to your local installation.
  3. Specify the Paths:
    • GROMACS Executable: Click the browse button (browse) to locate the GROMACS executable on your system (e.g., gmx.exe for Windows or gmx for Linux/macOS). SAMSON will verify the executable version. If it’s invalid, you’ll be notified.
    • Force Fields Directory: Locate the folder containing your forcefield.ff directories. Commonly, this folder resides at paths such as $HOME/gromacs/share/top/ on Linux/macOS.

    Custom GROMACS path

When Should You Use This Feature?

This functionality is ideal for local computations where you have complete control over your simulation environment. Please note that for cloud-based jobs, GROMACS Wizard defaults to its packaged version, and local settings aren’t relevant.

Additionally, having a precisely configured version of GROMACS can heavily influence the reproducibility of your molecular simulations—an essential factor for publishing and verifying your results.

Conclusion

Switching to a custom GROMACS version in SAMSON is a thoughtful feature that empowers users to adapt the toolkit to their exact molecular modeling requirements. This process ensures a more tailored and reproducible modeling workflow.

For more detailed instructions, check the full documentation page at https://documentation.samson-connect.net/tutorials/gromacs-wizard/settings/.

Note: 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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