One of the most frequent sources of friction in molecular modeling happens when you’re deep into a structure refinement or simulation, only to find you need to remove or add a few atoms. For many tools, this means stopping the simulation, reprocessing the molecular structure, and setting everything up again. But what if you could just do it live?
In SAMSON, when using the Universal Force Field (UFF) interaction model, you can delete and add atoms on the fly, and UFF will seamlessly recompute the system typization. This means you can tweak structures in real time and continue your simulations without restarting.
Simplified Editing Without Interruptions
Whether you’re refining a geometry, building a new molecule, or exploring conformational changes, the ability to make structural edits mid-simulation can be a huge time saver and a more natural modeling experience.
Deleting Atoms ✂️
To remove atoms during a UFF simulation:
- Select the eraser editor (look for the rubber icon).
- Click on the atoms you want to delete.
UFF will automatically recompute the system typization for the updated structure. No need for manual cleanup.
Adding Atoms ➕
You can also create and bond atoms directly to existing ones:
- Select an element from the periodic table editor within SAMSON.
- Click and hold on an existing atom in the simulation.
- Drag the mouse to where you want the new bonded atom.
- Release the mouse button — the new atom will appear connected and integrated in real time.
The transparency feedback instantly shows bonding as you move your cursor, giving you a clear visual cue before actual placement.
Live Typization Updates
UFF doesn’t just add or delete atoms — it adjusts its internal parameters accordingly, including recomputing atom types, bond orders, and related force field properties. This dynamic perception model makes UFF in SAMSON particularly well-suited for interactive molecular design and real-time simulations.
When Is This Useful?
- Fixing model errors without restarting a simulation.
- Exploring reaction intermediates by adding/removing atoms mid-pathway.
- Teaching environments where showing immediate change is valuable for engagement.
- Quick prototyping of functional groups before starting a full analysis.
This approach makes editing a molecule feel as smooth as sketching on paper — only here, all changes are structurally and energetically analyzed in real time.
To learn more, visit the original documentation page here: https://documentation.samson-connect.net/tutorials/uff/uff/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.