A molecular model can look ready to simulate and still contain details that need attention: bonds may be missing or incorrect, bond orders may be uncertain, and atoms need types before a force field can assign interactions. Sorting these out is a common source of friction when preparing a system. SAMSON’s Universal Force Field (UFF) workflow can automatically perceive bonds, bond orders, and atom types, then let you inspect and customize that setup before running a simulation.
This guide focuses on a useful habit: treat force-field setup as a sequence of checks, not just a button press. Automatic perception helps you get started, while the parameter window gives you a place to review the resulting model and adjust it when needed.
Start with the bond information you trust
Open the molecular system you want to work with, then add a simulator through Edit > Simulate > Add simulator. Select Universal Force Field, choose a state updater such as FIRE, and confirm. In the UFF setup window, decide whether to check Use existing bonds.
- Check the option when you want UFF to rely on the bonds already present in the model.
- Leave it unchecked when you want UFF to recompute bonds from atom types and positions.
This choice matters because it determines whether existing connectivity is retained or bond perception is part of initialization. If the software detects inconsistencies, it may show a warning. Treat that message as a reason to review the structure rather than simply proceeding without checking.
During initialization, UFF computes covalent bonds if needed, then computes bond orders and atom types. Once this is complete, the UFF parameter window appears.
Run the simulation and read the energy display
Start the simulation with Edit > Simulate > Start. The UFF window displays the energy contributions from individual terms as well as the total UFF energy. This is useful feedback while you work: you can interactively move atoms and observe how the model responds by updating the positions of other atoms.
UFF also exposes several settings that can be adjusted during use:
- Bond stretch interaction: choose Harmonic or Morse.
- van der Waals cutoff: set the distance limit for considering van der Waals interactions.
- Switching distance: set where the van der Waals term begins to be weighted so that it reaches zero smoothly at the cutoff.
- Neighbor-list construction periodicity: set how often the lists used for van der Waals interactions are recomputed. By default, they are recomputed at each time step.
If you are new to the workflow, begin with the default settings and change one parameter at a time. That makes it easier to connect a change in the interface with the behavior you observe.
When automatic perception needs a correction
Some systems may need more control over atom typing or bond orders. UFF offers customization options, but the documentation recommends them for advanced users because misuse can lead to incorrect structures. You can set lower maximum coordination or valence values for individual atoms, force a selected bond to a chosen bond order, or assign a UFF type to selected atoms. Bond orders can be non-integer, and the available forced bond-order range is 0.1 to 3.9.
If a bond order or atom type must remain unchanged during another round of perception, use the corresponding Freeze control. To clear customizations, use the relevant Reset all buttons. Reset perception recomputes perception using the current customized settings and atom positions; positions matter because bond creation depends on atomic distances.
Atoms can also be added or deleted while the model is being edited, and typization is recomputed automatically. For example, adding an atom bonded to an existing atom keeps it connected to the system. If you need help building the structure, see the SAMSON User Guide: Building molecules.
The practical takeaway: check whether your model’s existing bonds should be trusted, pay attention to initialization warnings, and keep advanced typization changes deliberate. For the full setup details and references, learn more in the UFF tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.