The
definition includes: name and identification “serial” number of the
fragment (numbers based on the residue ID numbers from the PDB file),
and a list of atoms from the PDB file that belong to the fragment. This
enables the most flexible way to split any PDB file into several
fragments by selecting specific atoms from each residue included into
the simulation.
The section provides information about vibrational modes coupled to the
electronic excited state. The section contains: the vibrational mode
number and its wavenumber, electron-vibrational coupling, and the
vibrational decay rate. These properties of electronic excited states
can be obtained from quantum chemical calculations or empirically. Thus,
PyFREC provides a flexible way of integrating computed and experimental
data into a single simulation.