Dear all,
I use x2top to get topology of a capped carbon nanotube with 168 atoms using oplsaa force field. The output information about dihedreals shows as follows. Before cleaning: 1008 dihedrals There are 252 Ryckaert-Bellemans dihedrals, 0 impropers Using my own code, I also get 1008 proper dihedrals. After comparison, I find a rule how only 252 dihedrals are keep after cleaning. For example, if I have local structure: C1 C5 \ / C3 - C4 / \ C2 C6 My own code gives 4 proper dihedrals: C1-C3-C4-C5, C1-C3-C4-C6, C2-C3-C4-C5, and C2-C3-C4-C6. And I think x2top also does in this way before cleaning. So I have question: why x2top needs a cleaning step to remove three of these four dihedrals? During cleaning, which one of four dihedrals should be kept? Also according to my understanding, for the following structure C1 - C6 / \ C2 C5 \ / C3 - C4 there should be some improper dihedrals, e.g., C1-C2-C3-C4 etc., to keep these atoms on the same plane. Why x2top does not give any improper dihedrals? Thanks in advance, Best wishes, Zhongqiao Dept of Chem & Biomole National Univ of Singapore
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