During molecular modeling, geometry optimization is a crucial step for refining structures prior to simulation or analysis. SAMSON’s implementation of the FIRE (Fast Inertial Relaxation Engine) minimizer helps you accelerate this process. But what happens when atoms are moved manually while minimizing? 👇
Sometimes users adjust atoms interactively to explore conformational space or fix geometrical artifacts before or during minimization. When using the FIRE minimizer, this can occasionally lead to unexpected behavior in energy relaxation dynamics—especially if those movements interfere with the stored minimization history.
Why Minimization History Matters
FIRE speeds up convergence by maintaining a “history” of atomic velocities and forces to adjust motion. If you manually move atoms mid-minimization, the previous history may mismatch the new structure, potentially destabilizing the optimization or resulting in strange movement behavior. It’s like suddenly changing the direction of a rolling ball—the past momentum no longer applies.
Clearing the Minimization History
If you experience unexpected behavior after manually adjusting atoms, a simple but powerful step is to reset the FIRE minimization history. This clears stored data so that FIRE can start fresh from the current atomic configuration—with no conflicting memory of prior dynamics.
How To Do It
After moving atoms manually in the molecular editor or workspace:
- Open the FIRE Minimizer settings in your current simulation setup.
- Click the Reset button.
This action clears the velocity/force history used for adaptive step computation, allowing the engine to begin cleanly from the present arrangement.
When Should You Reset?
Consider using the Reset option in the following scenarios:
- You manually dragged atoms or changed geometry during minimization.
- The minimization seems unstable or doesn’t converge as expected after such changes.
- You’re using the FIRE minimizer in an interactive modeling workflow that combines manual and automated editing.
Need a Visual?
Below is a visual comparison between FIRE minimization and the traditional steepest descent method. In cases where you find FIRE acting in an odd way after user interactions, chances are the minimization history needs resetting.
Conclusion
If your FIRE optimizer isn’t behaving the way you expect, especially after interactive editing, don’t forget to try the Reset button. This small step can help improve the fidelity and performance of your geometry optimizations in SAMSON workflows.
Learn more about geometry optimization in SAMSON and the FIRE minimizer in the full documentation here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.