If you’ve ever found yourself watching a molecule slowly crawl towards equilibrium during a simulation, you’re not alone. Many molecular modelers start with raw or predicted structures and need to refine them before simulation. Geometry optimization is essential to remove unrealistic atomic overlaps and outliers, but the process can be slow—especially when using the steepest descent method.
This is where the FIRE Minimizer (Fast Inertial Relaxation Engine) can help.
Where Steepest Descent Falls Short
The steepest descent algorithm is a staple in molecular modeling for geometry optimization. It moves atoms in the direction of the gradient of the energy, which works reasonably well for small deformations. But when your system needs large-scale rearrangement—like untangling loops in a protein or relaxing coarse-grained models—it quickly becomes inefficient. Convergence slows dramatically as the energy gradient flattens out.
This inefficiency leads to a simple pain: waiting. When your workflow stalls because your molecule won’t settle into its energy minimum, everything downstream is delayed.
Why Use the FIRE Minimizer
FIRE helps get these structures minimized faster. It mixes gradient descent with momentum to accelerate convergence across flat energy landscapes. For molecular modelers dealing with complex geometries, FIRE is particularly adept at navigating large-scale atomic motions efficiently.
Here’s a side-by-side comparison from SAMSON’s documentation that illustrates the difference:
A Simple Setup
Using the FIRE Minimizer in SAMSON is straightforward:
- Load your molecular system from a file like PDB or MOL2.
- Add a simulator: Go to
Edit > Add Simulatorand choose your interaction model. - Choose FIRE from the State Updaters list.
From there, you can tweak parameters such as step size and update frequency. The FIRE Minimizer even allows you to fix the step size and reset its internal history if you manually move atoms during the optimization process.
When to Use FIRE
The FIRE Minimizer is ideal for:
- Pre-simulation cleanup
- Structural relaxation of noisy or predicted geometries
- Large molecular systems with complex internal motions
It integrates seamlessly with other SAMSON Extensions like the Molecular Restrainer, helping clean up structures derived from NMR or other experimental data.
Learn more in the original documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON here.