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

[Hu Zhongqiao]

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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