As a molecular modeler, ensuring the reproducibility of your computations is likely a top priority. However, reproducing simulations accurately sometimes requires using a specific version of software like GROMACS. Did you know that the GROMACS Wizard in SAMSON allows you to achieve this easily by enabling the use of a locally installed version of GROMACS? Here’s how you can make it work effectively for your computational needs.
Why use a custom GROMACS version?
The GROMACS Wizard in SAMSON comes with a recent version of GROMACS out of the box, saving you the hassle of installation. But if you have a particular version of GROMACS installed on your system, whether for compatibility with older projects or ensuring consistency in published research, you can quickly integrate it into the GROMACS Wizard.
Setting up your custom GROMACS version
The process is straightforward. Start by navigating to the Settings section of the GROMACS Wizard, which you can access by clicking on the Settings button at the top of the interface.
Within the settings, you will find the Use a different GROMACS version option. Check this option, and you will need to provide two paths:
- Path to the GROMACS executable: This is the location of the
gmx(Linux/macOS) orgmx.exe(Windows) file on your system. Use the browse button
to select the file. Once selected, the version of the executable will be displayed here. If the file is invalid, “invalid” will be shown instead. - Path to the force fields folder: This folder contains all the
forcefield.ffdirectories. A typical path might look like$HOME/gromacs/share/top/on Linux or macOS. An example of how this looks in the interface is presented below:
The benefits of a local setup
This setup grants you flexibility. You can seamlessly test or deploy simulations developed in earlier versions of GROMACS, ensuring consistent results. It also simplifies workflows for researchers who rely on standardized simulations for collaborative projects or published methodologies.
Important considerations
While using older versions of GROMACS ensures reproducibility, always ensure compatibility between your system’s libraries and the selected GROMACS version. Additionally, keep track of updates and improvements in newer versions of GROMACS, as these could enhance performance and accuracy in specific simulations.
If you’d like to explore more, we recommend checking the full documentation for GROMACS Wizard settings at this link.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net.