Running Joyce

When all input files (JOYCE's main input, topology and QM data files) have been produced, the program can be launched simply through the following command:
$\fbox{$>$\ \textit{go.joyce \textit{label} -e -v }}$
where label is a user defined name related to target molecule T, and a JOYCE3.0 input file named joyce.label.inp exists in the working directory. This input file will be automatically edited (through the -e option) with the vim editor, and changes to the commands contained therein can be made. When this file is saved and closed, JOYCE3.0 starts the parameterization. When the procedure is over, the .log file is again opened by the vim editor, so that results can be checked. All other files illustrated in the previous sections are created automatically in the same working directory.

The JOYCE parameterization protocol can be applied to a large variety of molecular targets (see main text), resorting to the general step-wise procedure briefly outlined in the following (more details in the rest of the manual).

Step 0: 0.a] By taking the optimized QM geometry, JOYCE creates a list of all RICS of the molecular target, storing them into the file in the proper format for successive steps.
0.b] In addition to all bonded RICs, automatically generated by the JOYCE3.0 code in 0.a], specific atom pairs required to represent specific intra-molecular non-bonded interactions can be included in the RICs collection.
Step 1: The set of selected RICs (either created in Step0 or imported from other sources) is used to retrieve all harmonic parameters at once, by minimizing the term of the objective function involving QM and FF Hessian matrices (see Section 7 for details).
Step 2: The final QMD-FF is eventually retrieved by assigning all harmonic constants derived in Step 1 and applying the FIRA [1,21] while minimizing the term of the objective function involving QM and FF energies, as computed along the QM torsional scan. Note that the combined use of specific non-bonded terms (see 0.b]) and FIRA is only possible since the JOYCE3.0 release.[28].

Please see templates where these steps are carried out at the JOYCE3.0 website. [13]