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.本数据集包含来自论文《基于β-环糊精（β-cyclodextrin）二聚体与三聚体及发光探针的主客体超分子体系晶体结构预测》中相关Gromacs分子动力学模拟所需的全部必要文件。四个核心体系N2@CD2[A]、PH-TBB2@CD2[A]、PH-TBB2@CD3[B]与PH-TBB2@CD3[C]的结构文件分别存放于tar.gz格式压缩包N2-CD2-A、PH-TBB2-CD2-A、PH-TBB2-CD3-B及PH-TBB2-CD3-C中。每个压缩包内的文件对应完整的分子动力学模拟流程：start.gro为将环糊精内容替换为发光探针后得到的初始结构；em.gro为能量最小化完成后的结构；nvt.gro为NVT系综模拟后的结构；npt.gro为NPT系综模拟后的结构；topol.top为体系拓扑文件。萘（naphthalene）、菲（phenanthrene）、叔丁基苯（tert-butylbenzene）及β-环糊精的拓扑文件分别存放在naft.itp、pantr.itp、tbb.itp与cd-charmm.itp文件中；上述分子对应的位置约束文件分别为posre-naft.itp、posre-pantr.itp、posre-tbb.itp及posre-cd.itp。能量最小化、NVT系综及NPT系综模拟的运行参数分别存于em.mdp、nvt.mdp与npt.mdp文件中。CHARMM-36力场可于charmm36.ff.tar.gz压缩包中获取。