Easily Switch to Your Custom GROMACS Version in SAMSON

For molecular modelers, the flexibility to choose specific software versions for simulations can be critical, especially when reproducibility and system compatibility come into play. If you’re using SAMSON’s GROMACS Wizard, you’ll be glad to know that switching to a custom GROMACS version is a straightforward process. This feature ensures you can harness the exact tools you need for your local computations while taking advantage of SAMSON’s integrative molecular design capabilities.

Why Use a Custom GROMACS Version?

While GROMACS Wizard comes preinstalled with one of the latest versions of GROMACS, there are scenarios where users may need to work with their own GROMACS version. For example:

  • You already have GROMACS installed on your system and want to utilize it without redundancy.
  • You require an older version of GROMACS for the sake of reproducibility in your simulations.

The solution? Simply point SAMSON to your local GROMACS executable and force fields folder. Here’s how.

Steps to Configure Your Custom GROMACS Version

To use a locally installed version of GROMACS in SAMSON, follow these steps:

  1. Launch the GROMACS Wizard and click on the Settings button located at the top.

    2. Open settings

  2. Under Settings, locate and check the option Use a different GROMACS version.
  3. Provide two paths for your setup:
    1. A path to your GROMACS executable (gmx.exe on Windows or gmx on Linux/macOS). Use the browse button to browse and select the executable. Once the executable is recognized, the version will be displayed. If the executable is unrecognized, an “invalid” message will appear.
    2. A path to the force fields folder containing forcefield.ff directories. This is typically located at $HOME/gromacs/share/top/ on Linux/macOS.

    Custom GROMACS path

Once configured, SAMSON will seamlessly use your custom GROMACS version for local jobs.

When Should You Opt for This Feature?

Custom GROMACS execution is most beneficial in scenarios where specific versions or configurations are required for simulation consistency or compatibility. This is particularly helpful if you’re working in collaborative environments where simulation conditions need to match or if your research requires the validation of results over legacy software versions.

Important Considerations

When switching GROMACS versions, always verify the compatibility of your simulation configurations. Testing your setup thoroughly can save time and prevent issues caused by unsupported features or file formatting mismatches between versions.

Learn More

Interested in exploring this feature further? Head over to the official documentation page, where you’ll find detailed instructions and additional insights into working with custom GROMACS configurations in SAMSON.

Note: 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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