Molecular modelers often seek versatility in their workflows, particularly when it comes to simulation tools. A common challenge involves using specific versions of GROMACS for reproducibility purposes or taking advantage of locally installed packages. Did you know that SAMSON’s GROMACS Wizard not only provides an integrated GROMACS environment but also allows users to customize it by setting their own local versions of GROMACS? Here’s how this works and why it’s useful for your research.
Why Use a Custom GROMACS Version?
While SAMSON ships one of the latest GROMACS versions with its GROMACS Wizard, scientists often need to use a different version for specific research purposes. Here are some scenarios where this feature will make a difference:
- Ensuring reproducibility in computational studies by aligning your setup with a specific GROMACS version used in earlier experiments.
- Leveraging pre-installed GROMACS packages for compatibility with your existing research environment.
- Adapting to system-level requirements that may be aligned with particular GROMACS builds.
How to Enable a Custom GROMACS Version
SAMSON makes the process straightforward. Access the Settings button at the top of the GROMACS Wizard interface to configure your custom version. Here’s what you’ll need to do:
- Set the path to your GROMACS executable: Find the desired GROMACS installation path on your system. For Windows users, this would typically involve selecting the
gmx.exeexecutable. On Linux and macOS, you’ll look forgmx. Once selected, SAMSON will verify your input (if the executable isn’t recognized, “invalid” will be displayed). - Specify the path to the force fields folder: Navigate to the directory containing the forcefield.ff folders. Commonly, this directory resides under $HOME/gromacs/share/top/ for Linux and macOS users.
Below is a visual example of this setup:
Helpful Tips for Customization
When using a custom GROMACS version:
- Take note of compatibility. If your executable isn’t recognized, you may need to verify the file paths or ensure that you’re pointing to an appropriate version.
- Align the force field directory with your project needs. Selecting the correct force field can significantly influence the outcomes of your simulations.
- Leverage the auto-verification features of SAMSON to confirm your setup before running local computations.
Your Path to Streamlined Workflows
Configuring a custom GROMACS version in SAMSON is particularly beneficial for researchers working in collaborative environments. It ensures compatibility, adaptability, and high reproducibility in molecular simulations, ultimately boosting efficiency.
Ready to dive deeper? Learn more in the original documentation page here.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.