A molecular structure can look plausible and still contain strained geometry or forces that make it a poor starting point for a simulation. The practical challenge is to relax the structure without mistaking a smoother-looking model for a physically validated one. In SAMSON, the FIRE (Fast Inertial Relaxation Engine) minimizer offers a way to perform geometry optimization using the interaction model already selected for the system.
FIRE is particularly useful when the structure is undergoing collective or large-scale motion. Compared with steepest descent, it can converge faster in these situations, including cases where the potential energy changes only modestly while the geometry continues to evolve. It is not a substitute for choosing an appropriate interaction model or checking the result; it is a minimization method that works with the interaction model in your SAMSON simulator.
A useful first step: minimize a small system
Before applying settings to a large structure, try the workflow on a small test system. This makes it easier to see what the minimization controls do and to distinguish actual molecular movement from how often the viewport refreshes. You can load a structure in a supported format such as PDB or MOL2. SAMSON’s Loading Molecules Guide and supported formats page provide more information about bringing structures into the platform.
Set up the minimization
- Open Edit > Add Simulator.
- Choose the interaction model appropriate for your task.
- In the State Updaters list, select FIRE.
The distinction between the interaction model and the state updater is important: the interaction model describes the forces used by the simulation, while FIRE is the updater that advances the geometry during minimization. The simulator combines them. For more on how these components fit together, see the simulators overview.
Understand the controls before tuning
Step size is the initial integration step for minimization. It is one of the settings to inspect when you are configuring the relaxation. The Steps setting controls how many FIRE steps are performed between viewport updates. In other words, it affects how frequently you see the progress displayed; it is not the total number of minimization steps. Increasing it gives less frequent but more pronounced visual updates, which can make ongoing movement easier to observe.
The optional Fixed setting forces the step size to remain constant. If you want to compare settings, change them deliberately and observe the resulting motion rather than assuming one setting is best for every system. The appropriate choice depends on the system and the interaction model; this tutorial does not prescribe universal numerical values.
Read the motion, not just the animation
The visual comparison below illustrates the difference between FIRE relaxation and steepest-descent relaxation. It can help you recognize why a method that handles collective motion efficiently may be useful in a particular cleanup workflow. The animation is a visualization of relaxation, not proof that a structure is experimentally correct or that every modeling concern has been resolved.
One detail matters during interactive work: if you manually move atoms while minimization is running, press Reset to clear the FIRE history. This avoids carrying the previous minimization history forward after you have changed the structure by hand.
Where this fits in a modeling workflow
FIRE is implemented as a SAMSON State Updater, so it can be used wherever an application or extension needs geometry optimization. For example, it is used by the Molecular Restrainer extension for energy minimization of NMR-derived structures. That is a useful reminder that relaxation can be part of a larger modeling procedure, rather than a standalone guarantee of structural validity.
For the complete setup and additional context, read the FIRE minimizer tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at samson-connect.net.