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MD-Tracks is a trajectory analysis toolkit for molecular dynamics and Monte Carlo simulations. It is designed to interact with several simulation codes that generate trajectory data: CP2K, CPMD, DLPOLY, GROMACS, LAMMPS. The trajectory output files are first converted into a in a uniform binary format, which can then be processed with a bundle of analysis scripts, e.g. for the analysis of vibrational spectra, diffusion constants, radial distribution functions, and so on.
HiPart is a program to analyze the electronic structure of molecules with fuzzy-atom partitioning methods. It now supports four schemes to define atomic partitions: the Becke scheme, the Hirshfeld scheme, the Iterative Hirshfeld scheme, and the Iterative Stockholder Analysis. Within each scheme the following quantities can be computed: atomic charges, atomic dipoles, quality of charges and dipoles with respect to the ESP, the atomic multipole expansion, net and overlap populations, bond orders, spin charges, atomic overlap matrices in the orbital basis and in the basis of contracted Gaussians.
Zeobuilder is a user-friendly GUI toolkit for the construction of advanced molecular models (biological, inorganic, reactants in a catalyst, ...). The program contains several advanced tools to build, align, manipulate and analyze molecular structures. Most of its novel functionality is based on a hierarchical data-structure of reference frames to represent a molecular structure. Furthermore, Zeobuilder is extensible. The core program is compact and nearly all of the functionality is implemented through a plug-ins.
TAMkin is a post-processing toolkit for normal mode analysis, thermochemistry and reaction kinetics. It uses a Hessian computation from a standard computational chemistry program as its input. CHARMM, CP2K, CPMD, GAMESS, GAUSSIAN, QCHEM and VASP are supported. Multiple methods are implemented to perform a normal mode analysis (NMA). The frequencies from the NMA can be used to construct a molecular partition function to derive thermodynamic and kinetic parameters.
Yaff is created to provide a good reference implementation of the force fields developed at the Center for Molecular Modeling at the Ghent University. In its current version, Yaff is general and flexible enough to handle a large variety of force field models.
MolMod is the underlying Python library for Zeobuilder, TAMkin, HiPart, MD-Tracks and other projects at the CMM. It contains several auxiliary modules for the development of molecular modeling programs.