Crystal structure prediction of host-guest supramolecular systems based on β-cyclodextrin dimers and trimers with luminescent probes

Here are the necessary files for theGromacs molecular dynamics of the  systems from the article"Crystal structure prediction of host-guest supramolecularsystems based on β-cyclodextrin dimers and trimers with luminescent probes".The structure files of the four main systemsN2@CD2[A], PH-TBB2@CD2[A], PH-TBB2@CD3[B] and PH-TBB2@CD3[C]are contained in the tar.gz archivesN2-CD2-A, PH-TBB2-CD2-A, PH-TBB2-CD3-B and PH-TBB2-CD3-C respectively.The content of the archive reflects the MD workflow performed:start.gro - the initial structure obtained by replacing the CD content with the luminescent probe;em.gro - the structure after energy minimization;nvt.gro - the structure after NVT step;npt.gro - the structure after NPT step;topol.top - the system topology file.The included topology ofnaphthalene, phenanthrene, tert-butylbenzene and β-cyclodextrinare in the filesnaft.itp, pantr.itp, tbb.itp, cd-charmm.itp.Their position restraints are inposre-naft.itp, posre-pantr.itp, posre-tbb.itp, posre-cd.itp.Run parameters for EM, NVT and NPT steps are in the files em.mdp, nvt.mdp, npt.mdp.CHARRMM-36 force field is in charmm36.ff.tar.gz.