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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