[gmx-users] How does x2top clean dihedrals?

[Hu Zhongqiao]

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

 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091008/8c2ca188/attachment.html>