A molecular fragment cheminformatics roadmap for mesoscopic simulation

Background Mesoscopic simulation studies the structure, dynamicsand properties of large molecularensembles with millions of atoms: Its basic interacting units (beads) are no longer the nuclei and electrons of quantum chemical ab-initio calculations or the atom types of molecularmechanics but molecularfragments, molecules or even larger molecular entities. For its simulation setup and output a mesoscopic simulation kernel software uses abstract matrix (array) representations for bead topology and connectivity. Therefore a pure kernel-based mesoscopic simulation task is a tedious, time-consuming and error-prone venture that limits its practical use and application. A consequent cheminformaticsapproach tackles these problems and provides solutions for a considerably enhanced accessibility. This study aims at outlining a complete cheminformaticsroadmap that frames a mesoscopic MolecularFragment Dynamics (MFD) simulation kernel to allow its efficient use and practical application.