[gmx-users] How x2top makes proper and improper dihedrals?
zhongqiao_hu at nus.edu.sg
Mon Oct 5 03:55:31 CEST 2009
I use x2top to get topology of a capped carbon nanotube with 168 atoms
using oplsaa force field. The output information about dihedreals shows
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:
C3 - C4
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
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
Thanks in advance,
Dept of Chem & Biomole
National Univ of Singapore
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