[gmx-users] How does x2top clean dihedrals?

Hu Zhongqiao zhongqiao_hu at nus.edu.sg
Thu Oct 8 05:28:13 CEST 2009

Dear all,


Sorry that I have to post this message similar to one posted several
days ago, for I have spent much time on thinking about it but still have
not got a credible explanation.


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


That means one-fourth of initial 1008 dihedrals are kept after cleaning.
After careful check, I find the rule how x2top cleans dihedrals.


For example, if I have local structure:
C1           C5
    \         /
     C3 - C4
    /         \
C2           C6


Initially four dihedrals are counted by x2top: C1-C3-C4-C5, C1-C3-C4-C6,
C2-C3-C4-C5, and C2-C3-C4-C6.  But after cleaning, three of them are
removed. But I don't clearly understand why three of them should be
removed. Did I lose anything or make a stupid mistake? Sorry that I am
not familiar with C code and so can not get answer from source code. Can
anyone give me some explanation? 


Thanks in advance,


Sincerely yours,


Zhongqiao Hu


Dept of Chem & Biomol Engineer

National Univ of Singapore


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