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.