[gmx-users] How x2top makes proper and improper dihedrals?

Hu Zhongqiao zhongqiao_hu at nus.edu.sg
Mon Oct 5 03:55:31 CEST 2009

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


Thanks in advance,


Best wishes,



Dept of Chem & Biomole

National Univ of Singapore


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