Fast geometry optimization with FIRE minimizer#
Geometry optimization is a core task in molecular modeling, helping you reach stable, realistic molecular structures that correspond to energy minima. The FIRE Minimizer (Fast Inertial Relaxation Engine) is a fast, efficient algorithm - especially for large-scale molecular motions - that helps fine-tune 3D geometries for simulations and molecular-design workflows.
This tutorial shows how to use the FIRE Minimizer SAMSON Extension, based on the method by Bitzek et al.1.
Why Use FIRE?#
- Faster than steepest descent, especially for collective motions.
- Works with any SAMSON interaction model.
- Ideal for pre-simulation cleanup and structural relaxation.
Getting Started#
- Log into SAMSON Connect.
- Visit the FIRE Minimizer Extension page and click Add.
- Restart SAMSON - your extension will be ready to use.
How to Use the FIRE Minimizer#
Step 1 - Load a Molecular System#
You can load molecules from the PDB, MOL2, or other supported formats.
Tip
Learn more: Loading Molecules Guide
Step 2 - Add a Simulator#
- Go to Edit > Add Simulator.
- Choose the interaction model you want.
- In the State Updaters list, choose FIRE.
Tip
Learn more: Simulators Overview
FIRE Minimizer Settings#
| Setting | Description |
|---|---|
| Step size | Initial integration step for minimization. |
| Steps | Number of FIRE steps between updating the viewport. |
| Fixed | Force the step size to remain constant (optional). |
Resetting the History#
If you manually moved atoms while minimizing and want to clear the FIRE history, press Reset.
FIRE vs. Steepest Descent#
FIRE offers significantly faster convergence than the steepest descent algorithm, especially when potential energy changes are small but geometry still evolves significantly (large-scale motions).
To visualize the progress more clearly, increase the Steps value for less frequent but more pronounced updates.
Integration in SAMSON Workflows#
FIRE is implemented as a SAMSON State Updater, so it can work in any app/extension that needs to perfrom geometry optimization. For example, it is used in Molecular Restrainer Extension to perform energy minimization of NMR-derived structures.
Need Help?#
Have questions or feedback? Feel free to reach out via the Forum, via e-mail, via the Feedback button in SAMSON, or by directly discussing with us.