One common challenge in molecular modeling is adapting molecular structures when atoms move during a simulation. Often, manually updating topologies like covalent bonds and atom types can slow down workflows and increase the chance of errors.
If you’ve ever tried to simulate a molecular system that changes as you interact with it — for example, dragging atoms into new positions, breaking or forming bonds, or modifying valence — you’ve likely run into the limitations of static modeling. This is where the Interactive Modeling Universal Force Field (IM-UFF) in SAMSON brings valuable improvements.
What is IM-UFF?
IM-UFF is an extension of the Universal Force Field (UFF) that allows for interactive modeling where topological changes can occur automatically as the simulation progresses. It is built for users who want to build, edit, and simulate molecular systems dynamically while being guided by physically-based interatomic forces.
Smooth Transitions Between Topologies
With IM-UFF, you can:
- Break covalent bonds by pulling atoms apart.
- Create new bonds by bringing atoms close together.
- Allow atom typizations and bond orders to evolve automatically based on atom positions.
This means you’re free to explore molecular configurations without needing to manually redefine the system’s structure at each step.
How It Works in Practice
Once IM-UFF is active and the simulation is running, you simply click and drag atoms. When atoms are displaced slightly, IM-UFF preserves existing bonds by adjusting atomic positions locally. But when you move atoms sufficiently, it breaks bonds and updates the molecular topology. This approach allows for intuitive, experiment-like modeling in real-time.
Managing van der Waals Interactions During Manipulation
The Keep vdW for manipulated option offers additional control. When checked, van der Waals forces are applied to the atoms you’re actively moving. When unchecked, these interactions are disabled for manipulated atoms, making it easier to connect atoms without interference from repulsive forces. For delicate, high-control interactions, this setting can significantly improve the user experience.
Energy Feedback as You Model
While adjusting your molecular system, you get real-time visual feedback of different energy components — bond stretching, angular terms, van der Waals, and more — and the total energy of the system. This acts as a very intuitive visual compass, helping you understand if your current configuration is physically plausible.
Why It Matters
Real-time topology updating not only saves time but also opens new paths for exploratory simulations, such as testing molecular assembly or reaction hypotheses in an intuitive way. Whether you’re teaching, prototyping, or just exploring, IM-UFF provides a flexible framework for guided experimentation.
To learn more, visit the full documentation page on Interactive Modeling Universal Force Field.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.