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Welcome to the JOYCE documentation.

JOYCE is an integrated and user-friendly tool for the parameterization of intra-molecular quantum mechanically derived force fields (QMD-FFs). The energy and its first and second geometrical derivatives obtained by Quantum Mechanical (QM) calculations for a number of conformations of a single molecule in its ground- or excited states are used to parameterize intra-molecular FFs, suitable for classical computer simulations.

A QMD-FF is built up by essentially three ingredients, namely:

  • A set of selected generalized (or redundant) internal coordinates (RIC), as bond lengths, angles, dihedrals or non-bonded distances, which completely define the molecular geometry;
  • A set of model potential functions associated with each RIC;
  • A set of parameters (force constants and RIC’s equilibrium values) which complete the definition of the model functions, settling molecular chemical specificity onto the FF functional.

As the first two points are regarded, JOYCE, a FORTRAN program, reads a trial FF file in which both all the selected RIC and the associated model functions, which define the intra-molecular potential, are specified. This file can be automatically generated by the JOYCE program, created by the user or built by standard MD software.

Currently, the supported format for the input FF file is the Gromacs .top.

The equilibrium values of the selected internal coordinates are read by the JOYCE program from a formatted file (.fcc or .fchk). Finally, the force constants are computed by the JOYCE procedure from the first and second derivatives again read from the same QM database.

For more details on how to use JOYCE check the Manual, the Templates or the Tutorials.

The JOYCE program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation (version3).

In its current version, JOYCE allows ready to use implementation of the FF compatible with GROMACS, LAMMPS and CHARMM MD engines (Compatible software).

For further information please contact us.

Contact emails

Mails: pablo.martinezm@uam.es, anna.piras@pi.iccom.cnr.it