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<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Dear all,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>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.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>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.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Before cleaning: 1008 dihedrals<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>There are 252 Ryckaert-Bellemans dihedrals, 0 impropers<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>That means one-fourth of initial 1008 dihedrals are kept
after cleaning. After careful check, I find the rule how x2top cleans
dihedrals.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<pre><font size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'>For example, if I have local structure:<o:p></o:p></span></font></pre><pre><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></pre><pre><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'>C1 C5<o:p></o:p></span></font></pre><pre><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'> \ /<o:p></o:p></span></font></pre><pre><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'> C3 - C4<o:p></o:p></span></font></pre><pre><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'> / \<o:p></o:p></span></font></pre><pre><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'>C2 C6<o:p></o:p></span></font></pre>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>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? <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Thanks in advance,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Sincerely yours,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Zhongqiao Hu<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Dept of Chem & Biomol Engineer<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>National Univ of <st1:place w:st="on"><st1:country-region
w:st="on">Singapore</st1:country-region></st1:place></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
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