<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:st1="urn:schemas-microsoft-com:office:smarttags" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv=Content-Type content="text/html; charset=us-ascii">
<meta name=Generator content="Microsoft Word 11 (filtered medium)">
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="country-region"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="place"/>
<!--[if !mso]>
<style>
st1\:*{behavior:url(#default#ieooui) }
</style>
<![endif]-->
<style>
<!--
/* Font Definitions */
@font-face
{font-family:SimSun;
panose-1:2 1 6 0 3 1 1 1 1 1;}
@font-face
{font-family:SimSun;
panose-1:2 1 6 0 3 1 1 1 1 1;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman";}
a:link, span.MsoHyperlink
{color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{color:purple;
text-decoration:underline;}
pre
{margin:0in;
margin-bottom:.0001pt;
font-size:10.0pt;
font-family:"Courier New";}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:Arial;
color:windowtext;}
@page Section1
{size:8.5in 11.0in;
margin:1.0in 1.25in 1.0in 1.25in;}
div.Section1
{page:Section1;}
-->
</style>
</head>
<body lang=EN-US link=blue vlink=purple>
<div class=Section1>
<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'>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'>Using my own code, I also get 1008 proper dihedrals. After
comparison, I find a rule how only 252 dihedrals are keep after cleaning.<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'>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?<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'>Also according to my understanding, for the following
structure<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'> C1 - C6<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 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>
<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'>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 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>
<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'>Best wishes,</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Zhongqiao<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 & Biomole<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:country-region w:st="on"><st1:place
w:st="on">Singapore</st1:place></st1:country-region></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
</body>
</html>