Molecule Tutorial: Optimize Water and Run Vibrations

You will optimize a water molecule, verify that the result is a minimum rather than an arbitrary geometry, and run a molecular vibration calculation on the relaxed structure. The final artifacts include the optimization trajectory, frequencies, modes, and IR/Raman spectra.

Before you start

Using one calculator for optimization and vibration keeps the stationary point and its curvature on the same potential-energy surface.

Step 1: Load water

Action. Open File → Library, type water into the search box, choose Insert on the Water entry, and click the viewport to place the molecule.

Expected state. The active tab contains one oxygen and two hydrogens in a bent geometry.

Checkpoint. Confirm the formula and atom count before calculating. A malformed or duplicated structure will produce a real calculation of the wrong system.

Step 2: Optimize the structure

Action. Switch to Calc, choose Optimization, set Level of theory to GFN2-xTB, and leave Dispersion on Default - D4. Keep the cell fixed, use the default optimizer for a sensible Library geometry, and start the run.

Expected state. A new optimization folder appears in Explorer with log.txt, result.json, an energy trace, and a trajectory. The active structure updates to the final geometry when the run completes.

Checkpoint. Open the final result and confirm converged: true. Inspect the trajectory if energy or geometry changes unexpectedly. A water minimum should remain bent, with O–H distances around 1 Å; exact values depend on the method and settings.

Step 3: Verify the minimum

Optimization only finds a stationary geometry under its convergence rule. Before treating the geometry as a minimum:

1. Confirm the calculation did not merely exhaust its step budget.
2. Confirm the final maximum force satisfies the requested threshold.
3. Use the final structure, not the initial Library geometry, for the next stage.

If you changed tabs during the run, open the final trajectory frame or optimized structure as the active structure before continuing.

Step 4: Calculate vibrations

Action. Choose Vibration. Confirm GFN2-xTB and Default - D4 are selected, keep a 0.01 Å displacement and two-point finite differences for this tutorial, and request frequencies plus IR and Raman outputs.

Expected state. The calculation folder contains frequency/mode data and spectrum artifacts such as vibrations.json, vibrations.traj, ir_spectrum.json, and raman_spectrum.json.

Checkpoint. Open the IR spectrum. The three internal modes should consist of a lower-frequency H–O–H bend and two higher-frequency O–H stretches. Translation/rotation modes can appear near zero because of finite-difference noise.

Check your result

A small near-zero negative mode can be numerical translation/rotation noise. A large imaginary internal mode indicates the structure is not a minimum on this model surface.

Common problems

For periodic relaxation, phonons, and electronic DOS, continue with Crystal Tutorial: Silicon. The convergence theory behind this calculation is documented in Geometry Optimization.