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

[David van der Spoel]

Hu Zhongqiao wrote:
> Dear all,
> 
>  
> 
> Nobody would like to give some clues for this question, even the 
> developer of the x2top code?
> 
x2top -h
Did you use the -alldih flag? For OPLS like force field all dihedrals 
are need, for gromos like ff only one dihedral per  bond is kept, that 
is why.

> 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 explanation?
> 
> Thanks in advance,
> 
> Sincerely yours,
> 
> Zhongqiao Hu
> 
> Dept of Chem & Biomol Engineer
> 
> National Univ of Singapore
> 
>  
> 
> 
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> 
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se