Elements of the User Input
The philosophy of the user input assumes maximal reuse of the provided
information. Therefore, the user defines properties of each unique
molecular fragment only once, and then those properties are reused by
PyFREC. The PyFREC is a command line tool (all input and output are text
files). The user provides definitions of molecular fragments and
parameters of the simulation (e.g. Förster simulations or quantum
dynamics, etc.) in the main user input file (Scheme 2). The main user
input file (Scheme 2) contains the following sections: “Methods”,
“Molecular System”, followed by the definitions of molecular
fragments. The section “Methods” defines the type of calculations to
be requested (e.g., calculation of electronic couplings or quantum
dynamics simulations). The “Molecular System” section defines general
parameters of the entire system (e.g., a PDB file with the complete
protein complex and type and parameters of the electrostatic screening
model used in the requested calculation). The next section, “Quantum
Dynamics”, provides the initial conditions and numerical integration
parameters of the simulation. In addition, properties of each molecular
fragment (e.g. excitation energies and transition dipole moments) are
provided in a separate input files for each fragment (Scheme 2). These
properties of the fragment are usually computed with the general purpose
electronic structure packages (e.g. Gaussian). Auxiliary scripts can be
used to convert electronic structure package outputs to PyFREC input
format.