PyRAMD scheme: a protocol for computing the infrared spectra of polyatomic molecules using ab initio molecular dynamics

Here are illustrative examples of how to compute molecular-dynamics-based vibrational infrared spectra of polyatomic molecules using PyRAMD software. The dataset includes the version of the software used (PyRAMD from https://gitlab.desy.de/denis.tikhonov/pyramd, obtained July 15, 2024) for running molecular dynamics (MD) and various examples of MD simulations that illustrate various analysis issues. The large-time-step correction applicability is shown with methane (CH4) as an example. The applicability of the regularized least-squares spectral analysis is demonstrated in the case of carbon dioxide (CO2). The scale factors for the MD are obtained using water, ammonia, methane, ethane, methylamine, and methanol as the training set of molecules. The scale factors were obtained at the BLYP-D3(BJ)/6-31G, PBE-D3(BJ)/6-31G, and PBEh-3c levels of theory. The whole procedure was demonstrated with protonated methane as a test case.