Many molecular modelers rely on GROMACS to simulate molecular dynamics because of its flexibility, performance, and open-source nature. While integrative platforms like SAMSON offer out-of-the-box integration with GROMACS, a common need arises: what if your project requires a specific version of GROMACS? Or what if your system is optimized for a custom GROMACS build?
If you’ve ever encountered compatibility issues, reproducibility requirements, or simply wish to take advantage of a GROMACS installation that’s already configured on your machine, you’re not alone. Fortunately, SAMSON’s GROMACS Wizard offers a straightforward way to work with your preferred GROMACS version.
Why use a custom GROMACS version?
- Reproducibility: Scientific projects often demand the use of specific software versions to ensure consistent and verifiable results.
- Compatibility: If your GROMACS workflows were validated with a particular version or patched binary, using that same version avoids portability issues.
- Performance: Custom builds may include architecture-optimized flags that enhance simulation speed on your hardware.
- Advanced Features: Some patches and plugins are only compatible with certain versions.
Setting it up in SAMSON
To configure a custom GROMACS build in SAMSON, open the GROMACS Wizard and click the Settings button at the top of the interface:
In the Settings dialog, under the GROMACS version field, check the option “Use a different GROMACS version”. You will then need to provide two paths:
- Path to the GROMACS executable. On Linux and macOS this is usually called
gmx, while on Windows it’sgmx.exe. You can browse to it using the folder icon. - Path to the force fields folder. This is where GROMACS stores its
forcefield.ffdata directories (typically something like $HOME/gromacs/share/top/ on Linux or macOS).
If the executable you’ve chosen is valid, the version number will appear next to the input field. If it’s unrecognized, you’ll see an “invalid” warning, prompting you to double-check the binary path.
Tips for using custom versions effectively
- Before linking an external version, ensure that GROMACS is properly installed and the executable is working from your terminal or command line.
- Make sure the force field directory includes the necessary parameter files for your simulations. Missing files could result in simulation errors or incomplete topologies.
- If running on a cluster or HPC environment, consider matching the GROMACS version you use locally and on the server for interoperability.
By accommodating custom GROMACS installations, SAMSON gives you the flexibility to tailor simulations to your specific needs while keeping the integrative experience streamlined.
Learn more about additional settings like performance tweaking parameters and maximum warning overrides in the full documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.