Internal Coordinates & Model functions

The RIC set used in the fitting procedure is read from an input topology file, usually named, $<$label$>$.stepN.top (vide infra). As discussed in some detail in Section 5.3, such a topology can be purposely edited by the user or taken from existing database, if available. The supported format for the input topology is the GROMACS  native .top format.[18] The input topology file may also contain intermolecular parameters such as point charges and Lennard-Jones (LJ) parameters (see Section 7 for details), as well as other specifications that are not directly related with the JOYCE fitting procedure. In this case, JOYCE simply re-writes this information in the output topology file, labeled $joyce.new.top$, without performing any changes.

A complete set of RICs may be automatically generated by JOYCE3.0 in a preliminary run and stored to an auxiliary formatted text file (.txt), named generated.IC. Such a complete set of RICs is created by JOYCE3.0 from the only information (molecular geometry, connection table, bond order, etc.) retrieved from the QM descriptors. The content can be pasted in a new topology file (e.g. $<$label$>$.step1.top) and used in a second run. We stress that although the automatically generated harmonic potential functions might be confidently employed for stretching and bending RICs in most cases, the automated assignment to dihedral coordinates of either harmonic or Fourier-like potentials (see Section 7 for a more complete discussion) is delicate and might require user intervention. For instance, when the molecular structure hides a peculiar coordination (e.g. in presence of transition metals), the user can manually refine such automatic choice, or resort to other tools, as those now distributed at the JOYCE3.0 website[13] or in similar repositories.[25,24]