md-vib-spectra-simulation

You compute a vibrational power spectrum from an MD trajectory by processing velocity data through velocity autocorrelation. This skill uses MLatom to calculate the autocorrelation and outputs the resulting spectrum as PNG plots and numpy arrays.

Yes, you can generate an IR spectrum directly from a SMILES string. The skill uses SMILES inputs to run on-demand MD simulations with GFN2-xTB, then calculates the IR spectrum via dipole autocorrelation using MLatom.

Supported input formats for calculating vibrational spectra include h5md trajectory files and XYZ/VXYZ coordinate files. You can also input SMILES strings to generate MD trajectories on-demand if you do not have existing data.

No, you do not need rdkit and xtb if you are calculating IR spectra from existing h5md files. These dependencies are only required when generating MD trajectories on-demand from SMILES inputs.

A power spectrum derives from velocity autocorrelation, while an IR spectrum derives from dipole autocorrelation. This skill uses MLatom to compute either or both from your MD trajectories, outputting the results as NPY arrays and PNG visualizations.