TABLE 1.

Tasks partition in the new auxiliary scripts of COBRAMM. Alternatively to the setup scripts, the already existing cobramm.prep script is still available and under development

Script		Task
cobramm.prep	cobramm‐solvatedchromo.py	Parametrize and solvate the chromophore with a solvent box
	cobramm‐equilibration.py	Minimize, heat and equilibrate the system at MM level
	cobramm‐droplet.py	Create a droplet of solvent surrounding the chromophore, partition the system in H‐M‐L layers and prepares the input for QM/MM optimization
	cobramm‐wignersampling.py	Prepare a distribution of geometries and momenta sampling the normal modes of the chromophore based on a Wigner distribution
	cobramm‐postwignerequilibration.py	Equilibrate the solvent around the geometries obtained by Wigner distribution and prepare the inputs for TSH
cobramm‐plot.py		Store and plot the result of a TSH dynamics
cobramm‐populations.py		Extract the population of the excited states from an ensemble of trajectories
cobramm‐runpumprobe.py		Setup and run vertical excitation along the simulated trajectories
cobramm‐pumprobespectrum.py		Convolute, store and plot the TA spectrum and perform additional post‐processing analysis