When setting up molecular simulations, fine-tuning parameters can be difficult to get right the first time. Whether you’re trying to replicate a consistent energy minimization routine or comparing sets of parameters, remembering what you changed—or worse, losing those carefully adjusted settings—can be frustrating.
Fortunately, the GROMACS Wizard in SAMSON simplifies energy minimization parameter management in a subtle but useful way. If you’ve ever lost track of your simulation settings between sessions or wished for an easy way to share configurations between projects, this feature is for you.
Managing Energy Minimization Settings: The Essentials
In the Minimize tab of the GROMACS Wizard, you’ll find a Parameters section which exposes frequently used settings, such as emtol (energy minimization tolerance). These defaults are good for many basic uses. However, if you want to adjust advanced options or reset the settings, you’ll want to open the Advanced parameters window.
Click on the All… button to access the full range of GROMACS minimization parameters.
Restore Defaults When Needed
Have you made too many adjustments and want to go back to square one? No problem. In the advanced parameters window, a simple click on the Reset button will restore all parameters to their default values. This is helpful if you’re testing new settings and want a clean slate without reloading the entire simulation.
Reusing and Sharing: Save Your Settings
You can save your adjusted parameters for future use by clicking the Save as… button, which exports them to an MDP file (GROMACS input configuration file). This means:
- No more repeated manual adjustments for frequent setups.
- You can share your configuration with lab colleagues or across group projects.
- Parameter logging can now be part of your workflow with clean, portable files.
Loading from Existing Files
Need to apply a consistent setup across multiple runs or extend from a previous workflow? The Load from file… button allows you to import an MDP file from another project. Whether that’s from an earlier step in your own work or shared from a teammate, this ensures a coherent and reproducible simulation pipeline.
What Happens When You Close SAMSON?
If you’re in a rush or tend to forget saving your work, here’s some breathing room: SAMSON will remember your modified parameters when closed and reopen with your last-used values. Still, it’s always good practice to save them as an MDP file when the configuration matters for later analysis or reproducibility.
Why It Matters
Being able to restore, save, and load parameters isn’t just about convenience—it’s about reducing errors, tracing back results, and building productive habits as simulations get more complex. These features offer much-needed control in a space where precision is essential.
To learn more about the broader context and how this fits into the full pipeline of running energy minimizations with the GROMACS Wizard in SAMSON, check out the full documentation page: Energy Minimization with GROMACS Wizard.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.