One of the common frustrations in molecular modeling is having to stop and manually reassign bonds and atom types every time you make a structural edit. Whether you’re building a new molecule, modifying a reaction intermediate, or fine-tuning a structure, maintaining consistent topology often feels more like a chore than a step forward.
If you’ve spent time manually removing and reassigning bonds to reflect changes in molecular structures during simulation or modeling, you’re familiar with how disruptive this process can be. Wouldn’t it be helpful to have a system that can handle these topological changes automatically, letting you focus more on your scientific goals and less on software fuss?
This is where the Interactive Modeling Universal Force Field (IM-UFF) becomes useful. Integrated into the SAMSON platform, IM-UFF extends the traditional Universal Force Field (UFF) to support real-time editing of molecular topology during simulation.
How It Works: Topology That Adapts
IM-UFF allows covalent bonds to be formed or broken automatically based on atomic positions, eliminating the need for manual updates to topology:
- If you move an atom slightly, the bond stretches—but doesn’t break. The structure locally adjusts.
- If you move it further, bonds to neighboring atoms break smoothly.
- When moving an atom close to others, new bonds can form if the spatial criteria are met.
The force field handles these changes smoothly, recalculating bond orders, atom types, and energies in real time. This makes modeling more intuitive and lets you iterate quickly: drag atoms, test pathways, or explore reactions, without worrying about resetting connectivity manually.
User Control: vdW Interactions and Static Topology
While IM-UFF is dynamic by default, two togglable options give you control:
- Static Topology (UFF only): If selected, the simulation uses standard UFF with fixed topology. If unselected, IM-UFF takes over and the topology becomes dynamic.
- Keep vdW for Manipulated: Normally when dragging an atom, its van der Waals (vdW) interactions are temporarily ignored to ease manipulations. If you check this option, all vdW interactions—including for the atoms you’re moving—will continue to be calculated.
This combination is particularly helpful in early-stage design, where you may want topological flexibility, but also need precise insights into the energetics and behavior of specific interactions.
Live Topology in Action
Here’s a short example from the IM-UFF simulation tutorial in SAMSON, showing how molecular topology adapts during interaction:
As you can see, bonds stretch, break, and form in real time, all while maintaining a continuous energy profile. It’s a responsive, physics-based experience that supports a more fluid modeling workflow.
Is It Customizable?
Yes. You can adjust:
- vdW cutoff distances and switching functions
- Frequency of neighbor list updates
- Maximum coordination and valence (when dynamic topology is active)
During full IM-UFF simulations, bond orders and atom types become continuous, based on position. You don’t directly set them—instead, the model continuously adapts as atoms move. This approach is useful for capturing transitions between bonding patterns more realistically.
Give It a Try
If you often edit structures and feel constrained by force fields that fix topology in place, IM-UFF adds a level of interaction that can help speed up both exploration and prototyping. Try dragging atoms, testing different geometries, or building structures atom-by-atom without worrying about manually updating bonding information—SAMSON and IM-UFF will take care of it for you.
To learn more about the underlying methods and options, visit the full tutorial here: Interactive Modeling Universal Force Field (IM-UFF) Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.