Editing molecular systems during a simulation is something many computational chemists and structural biologists wish they could do more freely. Unfortunately, traditional force fields assume fixed topologies, making dynamic changes — like the formation or breaking of covalent bonds — either impossible or awkward to implement.
But what if you could safely and interactively edit molecules using physically-based interactions — without having to stop the simulation?
That’s exactly what the Interactive Modeling Universal Force Field (IM-UFF) in SAMSON offers.
The Challenge: Editing Systems Without Breaking Simulations
In traditional force-field simulations, molecular systems have fixed bonds and atom types. This is fine for static or very controlled systems, but becomes limiting when you’re designing new molecules, modeling reactive processes, or simply exploring structural transformations.
For example, dragging an atom too far might break a connection in your mind — but in a traditional simulation, the bond remains unless you manually remove it. Or worse, the system becomes unstable or downright crashes. Scenarios like modeling a chemical reaction or docking a ligand while maintaining physical realism become difficult.
The IM-UFF Solution
The IM-UFF interaction model is an extension of the Universal Force Field (UFF) developed specifically for interactive modeling. It allows the system’s topology to change during a simulation, meaning bonds can automatically form or break as atoms are manipulated.
Here’s how it works in practice:
- You manipulate atoms directly with your mouse.
- The system continuously evaluates distances and energy interactions (including bond strength and van der Waals interactions).
- If atoms move apart sufficiently, bonds break smoothly; if atoms approach viable bonding distances and angles, new bonds can form.
- Typizations (i.e., atom types and bond orders) are updated automatically to reflect the evolving structure.
This is possible because IM-UFF computes bond order and atom types as continuous functions of atomic positions — a key departure from the discrete assignments in standard UFF.
Minimal Setup, Instant Feedback
You don’t have to go through complex configuration menus. IM-UFF is designed for ease of use. Simply add a simulator in SAMSON via Edit > Simulate > Add simulator (or use Ctrl+Shift+M), and choose Interactive Modeling Universal Force Field. Start the simulation and begin editing your model with immediate visual and physical feedback.
Want to tweak things further? IM-UFF includes additional controls:
- Keep vdW for manipulated: Can be turned off to ignore van der Waals forces when you’re manually moving atoms, making it easier to connect new atoms.
- Static topology: Toggle this option if you temporarily want to simulate your system with fixed bonds (standard UFF behavior).
Watch It In Action
Here’s an example of IM-UFF handling structural changes during an interactive session:
A Small Shift, A Big Difference
One important technical note: to ensure physical consistency, IM-UFF modifies the zero-energy reference compared to standard UFF. In standard UFF, the bond energy is zero at equilibrium. In IM-UFF, it’s zero at infinite distance. This change helps avoid inconsistencies in energy evaluation, especially when switching back and forth between fixed and dynamic topologies.
Applications and Benefits
IM-UFF is especially useful if you’re working in any of the following areas:
- Computational drug design
- Reaction modeling
- Educational tools that involve hands-on molecular construction
- Interactive teaching demos of molecular behavior
You no longer need to set up new simulations every time a bond changes — just interact with the system in real time.
To learn more about the IM-UFF interaction model or advanced options like parameter customization, check out the full documentation: https://documentation.samson-connect.net/tutorials/uff/im-uff/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.