Geometry optimization is a common step in molecular modeling, but it can often be painfully slow — especially when working with large molecules or structures that require considerable relaxation before simulations. If you’ve been relying on the classic steepest descent algorithm and find yourself waiting too long for convergence, there may be a faster alternative in the SAMSON platform: the FIRE Minimizer.
The FIRE (Fast Inertial Relaxation Engine) minimizer is designed to cut down on optimization time, particularly for geometry transformations involving large groups of atoms. It’s ideal when potential energy gradients are small, but atomic positions still need to move significantly to reach a stable structure.
Understanding the Challenge
The steepest descent method updates atomic positions in the direction of the greatest energy descent, but it does so in a very localized and conservative way. For collective motions — like when an entire domain shifts or ring systems tilt — steepest descent takes many small steps that can drastically increase computation time.
Why Use FIRE Instead?
- Faster progress for problems involving collective atom motion.
- Smoother relaxation of structures, especially when optimizing imported or experimental geometries.
- Compatible across SAMSON — FIRE can be used with any SAMSON interaction model and apps.
The following comparison shows a side-by-side visualization of a structure being relaxed using FIRE and steepest descent:
When Should You Use FIRE?
If you’re doing any of the following, switching to FIRE might save you noticeable time and give you better results:
- Optimizing NMR-derived or imported structures with non-ideal geometries.
- Running simulations that require quick relaxation during setup.
- Batch-processing multiple molecules for energy minimization before simulation.
How to Learn More
FIRE is available as a minimization feature in SAMSON simulators and is used in extensions like Molecular Restrainer. You can tweak parameters such as step size, fixed step behavior, and viewport update frequency to better fit your workflow.
Learn more and explore a complete guide on how to use it in this FIRE Minimizer tutorial.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download the platform at https://www.samson-connect.net.