When working with force fields in molecular modeling, one common challenge is handling systems where automatic perception of atom types and bond orders fails. This can happen during the modeling of new compounds, structures with unconventional bonding, or even systems with partial charges or constrained geometries. If the force field misinterprets the atomic connectivity, the resulting simulations can become meaningless.
The Universal Force Field (UFF) module in SAMSON addresses this issue by allowing users to fully customize the typization process. If you’ve reached the limits of automation and accuracy in your molecular simulation workflows, this post walks you through how you can manually tweak atom types, bond orders, coordination, and valence values using UFF in SAMSON.
Why Custom Typization Matters
Automatic perception is great—but it’s not always right. Especially for edge-case molecules, reactive intermediates, or fragments with unusual bonding. Having the option to manually override how a molecule is interpreted allows you to:
- Ensure realistic energy calculations
- Preserve critical structural data during optimization
- Improve convergence in sensitive simulations
What Can Be Customized in UFF
Once you load a system in SAMSON and launch a UFF simulation, the parameter window lets you go deeper than default settings:
- Maximum coordination and valence: You can lower the values atom-by-atom to refine how the atom’s bonding environment is perceived. Only values lower than the default are effective.
- Bond orders: Select a bond (or multiple), assign it a new bond order (values between 0.1 and 3.9), and click Set. You can then lock this value to prevent future perception rounds from modifying it using the Freeze button.
- Atom types: Similarly, select atoms, assign them a UFF type, then press Set. Freeze these to maintain manual settings after structure updates.
Restoring Defaults and Recomputing Perception
If you want to go back, simply use the Reset All buttons to clear bond orders, atom types or coordination constraints. You can then hit Reset Perception to recompute the molecular structure from the current positions and user-defined customizations.
This flexibility can be especially helpful in systems where certain variables must be fixed for experimental consistency or where molecular topology needs to stay rigid. It’s powerful, but also easy to override the automatic behavior only when needed, maintaining a useful balance between accuracy and control.
When to Use This
This feature is most useful when:
- Your atom typization is incorrect after initial setup
- You are modeling organometallic or exotic coordination compounds
- Bond order resonance or partial bonding is important
- Your system cannot be optimized correctly due to atypical connectivity
With a few clicks, UFF in SAMSON lets you fix these without rebuilding your molecule from scratch.
To learn more and explore other features of the UFF module, visit the UFF tutorial page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON directly at https://www.samson-connect.net.