[gmx-users] Why does x2top need to clean dihedrals?

Hu Zhongqiao zhongqiao_hu at nus.edu.sg
Fri Oct 9 03:36:19 CEST 2009

Dear all,


Nobody would like to give some clues for this question, even the
developer of the x2top code?

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 understand why three of them should be removed. Do
I 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

Thanks in advance,

Sincerely yours,

Zhongqiao Hu

Dept of Chem & Biomol Engineer

National Univ of Singapore


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