How to Use a Custom GROMACS Version in GROMACS Wizard

Molecular modelers often face challenges when trying to ensure reproducibility or optimize their computational setup for molecular dynamics simulations. One recurring challenge is the need to use a specific version of GROMACS, particularly when the packaged version does not meet local requirements. In this blog post, we’ll explore how to configure GROMACS Wizard in SAMSON to use a custom GROMACS version installed on your machine, helping you achieve both flexibility and reproducibility in your workflows.

Why Use a Custom GROMACS Version?

Although GROMACS Wizard comes packaged with one of the latest GROMACS versions, there are scenarios where you might want to use a custom version:

  • Ensuring reproducibility by aligning with the version used in your published work or ongoing collaborations.
  • Taking advantage of optimizations or features in specific GROMACS releases.
  • Integrating a GROMACS installation already tailored to your local hardware or custom needs.

If this sounds like your use case, read on to learn how you can do this with GROMACS Wizard.

Step-by-Step Guide

1. Open the Settings Panel

To get started, open the GROMACS Wizard in SAMSON and click on the Settings button at the top. This will open a panel where you can configure your GROMACS setup.

Open settings

2. Select a Custom GROMACS Version

By default, the Settings display the version of the packaged GROMACS included with the wizard. To switch to a custom version, follow these steps:

  1. Check the box labeled Use a different GROMACS version.
  2. Specify the path to your locally installed GROMACS executable by clicking on the browse button (browse). Accepted executable names are gmx.exe (Windows) or gmx (Linux/macOS). The wizard will verify the version for compatibility, showing “invalid” if it is unrecognized.
  3. Set the path to the force-field directory containing forcefield.ff folders. For example, this could be located under $HOME/gromacs/share/top/ on Linux/macOS systems.

Custom GROMACS path

3. Verify Your Configuration

Once you’ve specified the executable and force-field path, double-check that the correct version is displayed, and that your configurations align with the intended setup. If everything checks out, you’re ready to run local calculations using your custom GROMACS build.

Additional Tips

When using a custom GROMACS version, you might encounter warnings related to force fields or configurations, especially with certain workflows such as GROMOS-based simulations. Some warnings are harmless, but it’s advised to interpret them carefully to avoid generating unstable systems. You can bypass specific warnings by using the -maxwarn option in the GROMACS Wizard settings.

Explore More

Configuring a custom GROMACS version gives molecular modelers flexibility, whether for improving simulation performance, achieving reproducibility, or simply aligning with personal preferences. SAMSON makes this process easy through its intuitive interface and customizable settings. For more information about additional parameters you can tune, visit the official documentation.

SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON now at samson-connect.net.

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