A molecular structure can look close to reasonable and still contain strained geometry. Before running a simulation, modelers often need to relax the structure so it can settle toward a lower-energy arrangement. The frustrating part is that a minimizer may appear to make little progress—particularly when many atoms need to move together.
The Fast Inertial Relaxation Engine (FIRE) minimizer is one option for this situation. It is designed to converge faster than steepest descent in many cases, especially when the geometry changes through large-scale or collective motions. Here’s a practical way to add it to a SAMSON workflow, and how to think about its controls.
Set up a small, clear test
Start by loading a molecular system from a supported format such as PDB or MOL2. If you are learning the controls, use a small test system first: it makes the effect of your settings easier to see. Then open Edit > Add Simulator, select the interaction model you want to use, and choose FIRE from the State Updaters list.
This order matters conceptually: the interaction model supplies the model of the system’s interactions, while FIRE is the state updater used to perform the geometry optimization. FIRE is not tied to just one interaction model; it can work with any SAMSON interaction model.
Understand the controls before tuning them
- Step size is the initial integration step for minimization. It is a starting control for how the minimizer advances.
- Steps sets how many FIRE steps occur between viewport updates. It changes how often you see updates—not the number of steps in the minimization as a whole.
- Fixed optionally keeps the step size constant.
If the motion is difficult to follow, try increasing Steps. The viewport will update less frequently, but each update can show a more noticeable change. This is a way to make progress easier to inspect; it is not, by itself, a change to the underlying interaction model.
Why compare FIRE with steepest descent?
Steepest descent is a familiar route to energy minimization, but it can be slow when the structure is evolving through large-scale motions even as potential energy changes only a little. FIRE can be a useful alternative in that situation. The comparison below shows the two relaxation animations; the exact behavior depends on the molecular system and the settings used.
A small but important workflow detail
Interactive modeling can mean moving atoms by hand while minimization is underway. If you do that and want to clear FIRE’s history, press Reset. This is especially worth remembering when the motion you see no longer reflects only the minimizer’s response to the current structure.
FIRE is implemented as a SAMSON State Updater, so it can also be used by apps or extensions that need geometry optimization. One example is the Molecular Restrainer extension, which uses FIRE for energy minimization of NMR-derived structures. That makes the minimizer relevant not only for a standalone cleanup, but also as part of a broader modeling workflow.
A useful starting routine is therefore simple: choose your interaction model, add FIRE as the state updater, observe the relaxation, and adjust the viewport update frequency if it is hard to follow. If you manually intervene, reset the FIRE history. For the full setup and additional context, read the FIRE minimizer tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.