[gmx-users] How does x2top clean dihedrals?
zhongqiao_hu at nus.edu.sg
Thu Oct 8 05:28:13 CEST 2009
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
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:
C3 - C4
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,
Dept of Chem & Biomol Engineer
National Univ of Singapore
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