Before You Relax a Structure: A Practical UMA Checklist

A molecular structure can be ready for refinement and still produce confusing results if the model is set up for the wrong kind of system—or if important inputs such as charge, spin, or the periodic cell are overlooked. UMA Force Field in SAMSON offers interactive energy and force evaluation, but getting useful feedback starts with a few deliberate choices.

This guide focuses on a practical question: how can you use UMA to explore a structure without mistaking a setup issue or an exploratory estimate for a final answer?

Start by matching the task to the system

When you add a simulator through Edit > Simulate > Add simulator, select UMA Force Field and choose a state updater, such as FIRE. In the UMA Force Field Setup window, you then choose a model and task. The task should reflect the kind of system you are evaluating:

  • OMOL – Molecules for molecular systems.
  • OMAT – Inorganic materials for bulk inorganic materials.
  • ODAC – MOFs for MOFs and direct-air-capture-style adsorption workflows.
  • OC20 – Catalysis for catalytic surfaces and adsorbates.
  • OMC – Molecular crystals for molecular-crystal systems.

This choice is more than a label: it defines the application domain used for the evaluation. For molecular systems, OMOL is also the task whose interface uses total charge and spin multiplicity.

UMA Force Field Setup window showing model and task choices

Choose a model for the first pass

The extension offers UMA-S in two sizes—2.3 GB, version 1.2, and 1.1 GB, version 1.1—and UMA-M at 11.7 GB, version 1.1. For a first interactive workflow, the documentation recommends starting with UMA-S unless you already know you need the larger UMA-M model. This keeps the initial decision simple: begin with the default fast option, then choose a larger model when your work calls for it.

Before starting, confirm that the UMA Force Field and Python Scripting extensions are installed and up to date, and that the computer can install Python packages on first use. Initial setup may take time because UMA prepares a dedicated Python environment and may request access to the models. Follow SAMSON’s prompts; once setup finishes, you may need to create the interaction model again.

Give the first evaluation time to finish

Once the UMA Properties window appears, start the simulation with Edit > Simulate > Start. Wait for the first evaluation before interpreting the energy. At startup, the interface may briefly report that energy is unavailable; the total energy appears after the first evaluation succeeds. After that, you can move atoms or refine the structure while UMA updates energies and forces.

UMA Properties window after startup

Check the inputs that change interpretation

For OMOL, set total charge and spin multiplicity to values consistent with the molecular system you intend to model. These settings are part of the request sent to UMA, so they should not be treated as incidental display options.

For periodic workflows, check whether periodic boundary conditions are enabled and verify the 3 × 3 cell matrix in angstroms. A cell that does not represent the intended structure can make subsequent interpretation unreliable. The interface provides the controls; checking that they match your system is part of preparing the calculation.

UMA periodic boundary condition controls and cell matrix

Use bond updates as exploration, not proof

The Bond update setting controls how the bond graph is handled during simulation. Covalent recomputes covalent bonds from the current structure; Off leaves the current graph unchanged. Wiberg and Mayer options estimate bond orders with a deep-learning model. These estimates can help visualize changes during interactive exploration, but they are not a substitute for confirming an important chemical conclusion with an appropriate reference method.

A simple decision sequence

  1. Choose the task that matches the system.
  2. Start with UMA-S for rapid feedback.
  3. For OMOL, check charge and spin multiplicity.
  4. For periodic systems, verify the cell and PBC setting.
  5. Wait for the first evaluation, then explore or refine the structure.
  6. Use UMA to screen and explore; confirm final results with a higher-accuracy reference method when needed.

This sequence helps separate three different questions: whether the setup matches the system, whether the first evaluation has completed, and how much confidence to place in an exploratory result.

For the full setup instructions and additional details, see the UMA Force Field tutorial.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.

Comments are closed.