Output files

When the parameterization finishes normally, JOYCE3.0 produces two main output files and some optional auxiliary files. The main outputs are a log and a topology file, whose defaults names are joyce.label.out and , respectively.

$\cdot$: The log file contains all information about the fitting procedure, with a detailed analysis of employed RIC, normal modes, involved vibrational frequencies, residues and standard deviation.
$\cdot$: The default output topology file always gets the default name and contains all parameters of the intramolecular term of the QMD-FF. It can be used as such in gas-phase simulations with the GROMACS [18] engine.

As reported in more detail in Section 7, JOYCE3.0 QMD-FF parameters can in principle be employed with any MD code, provided the same model potential functions are implemented in the MD engine. Within the current distribution, two tools can be found[13] to automatically convert the final JOYCE3.0 topology in formats compatible to MD software other than GROMACS , namely the popular CHARMM [11] and LAMMPS [26] engines. Yet, users are strongly encouraged to resort if possible to the GROMACS engine, as only the format supports the full list of JOYCE3.0 model potential functions, hence allowing to fully exploit QMD-FF accuracy, in particular when dealing with large flexible targets. Furthermore, other auxiliary files are produced by the JOYCE run, namely a generated.IC, an assign, and dependence file. All these are intended as work scratch files, and can be "copied & pasted" in the main input files for successive runs.

$\cdot$: The generated.IC.txt file, contains a list of all IC which can be naturally retrieved from the T molecular geometry and its connection table. Note that it also contains by default all the non-bonded intramolecular non-bonded interactions (see Section 7), constructed from the optimized geometry and the intermolecular parameters (charges and LJ ) found in the input topology.
$\cdot$: The assign.dat files contains the values of all parameterized force constants, and it can be pasted in the JOYCE main input file and used in a successive fitting, in which, for instance, some force constants may be fixed during the parameterization procedure. As detailed in Section 4, this assignment is routinely exploited when applying the two-step JOYCE procedure. Further details can be found at the JOYCE3.0 website.[13]
$\cdot$: The suggdeps.txt file contains suggested dependencies between FF parameters, dictated by symmetry, chemical equivalence or transferability. This file can be pasted in the JOYCE main input, for a successive fitting where the values of selected force constants will not be independently varied during the parameterization and their ratio is kept constrained (see JOYCE tutorials at the website for further details. [13]
$\cdot$: Several .dat files, containing several data to be plotted for inquiry and validation purposes, such as the QM and QMD-FF torsional energy profiles.
$\cdot$: Upon request, JOYCE3.0 can also prepare some graphs, directly saved as .agr files compatible with the XmGrace graphical software, [27] containing comparison of relevant data computed either with the QMD-FF or with the reference QM method. The interested reader can visit the JOYCE3.0 website[13] for further information and templates.

All the aforementioned JOYCE's input and output files are described in some detail in the next sections.