<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=Content-Type content="text/html; charset=gb2312">
<META content="MSHTML 6.00.6000.16674" name=GENERATOR>
<STYLE>@font-face {
font-family: 宋体;
}
@font-face {
font-family: Verdana;
}
@font-face {
font-family: @宋体;
}
@page Section1 {size: 595.3pt 841.9pt; margin: 72.0pt 90.0pt 72.0pt 90.0pt; layout-grid: 15.6pt; }
P.MsoNormal {
TEXT-JUSTIFY: inter-ideograph; FONT-SIZE: 10.5pt; MARGIN: 0cm 0cm 0pt; FONT-FAMILY: "Times New Roman"; TEXT-ALIGN: justify
}
LI.MsoNormal {
TEXT-JUSTIFY: inter-ideograph; FONT-SIZE: 10.5pt; MARGIN: 0cm 0cm 0pt; FONT-FAMILY: "Times New Roman"; TEXT-ALIGN: justify
}
DIV.MsoNormal {
TEXT-JUSTIFY: inter-ideograph; FONT-SIZE: 10.5pt; MARGIN: 0cm 0cm 0pt; FONT-FAMILY: "Times New Roman"; TEXT-ALIGN: justify
}
A:link {
COLOR: blue; TEXT-DECORATION: underline
}
SPAN.MsoHyperlink {
COLOR: blue; TEXT-DECORATION: underline
}
A:visited {
COLOR: purple; TEXT-DECORATION: underline
}
SPAN.MsoHyperlinkFollowed {
COLOR: purple; TEXT-DECORATION: underline
}
SPAN.EmailStyle17 {
FONT-WEIGHT: normal; COLOR: windowtext; FONT-STYLE: normal; FONT-FAMILY: Verdana; TEXT-DECORATION: none; mso-style-type: personal-compose
}
DIV.Section1 {
page: Section1
}
BLOCKQUOTE {
MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px; MARGIN-LEFT: 2em
}
OL {
MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px
}
UL {
MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px
}
</STYLE>
</HEAD>
<BODY>
<DIV><FONT face=Verdana color=#0000ff size=2>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: left; mso-pagination: widow-orphan"
align=left><SPAN lang=EN-US
style="FONT-SIZE: 10pt; COLOR: black; FONT-FAMILY: Verdana; mso-font-kerning: 0pt; mso-bidi-font-family: 宋体"><?xml:namespace
prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p>Hi
all,</o:p></SPAN></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: left; mso-pagination: widow-orphan"
align=left><SPAN lang=EN-US
style="FONT-SIZE: 10pt; COLOR: black; FONT-FAMILY: Verdana; mso-font-kerning: 0pt; mso-bidi-font-family: 宋体"><o:p></o:p></SPAN> </P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: left; mso-pagination: widow-orphan"
align=left><SPAN lang=EN-US
style="FONT-SIZE: 10pt; COLOR: black; FONT-FAMILY: Verdana; mso-font-kerning: 0pt; mso-bidi-font-family: 宋体"><o:p>Recently,
I post one question about g_rdf under Version 3.3.3. After discussing with
Florian Dommert, and rereading the code of gmx_rdf.c, I have the following
results:</o:p></SPAN></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: left; mso-pagination: widow-orphan"
align=left><SPAN lang=EN-US
style="FONT-SIZE: 10pt; COLOR: black; FONT-FAMILY: Verdana; mso-font-kerning: 0pt; mso-bidi-font-family: 宋体"><o:p></o:p></SPAN></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: left; mso-pagination: widow-orphan"
align=left><SPAN lang=EN-US
style="FONT-SIZE: 10pt; COLOR: black; FONT-FAMILY: Verdana; mso-font-kerning: 0pt; mso-bidi-font-family: 宋体">1.
-nocom -rdf atom is reliable;<o:p></o:p></SPAN></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: left; mso-pagination: widow-orphan; mso-char-indent-count: 1.0"
align=left><SPAN lang=EN-US
style="FONT-SIZE: 10pt; COLOR: black; FONT-FAMILY: Verdana; mso-font-kerning: 0pt; mso-bidi-font-family: 宋体">2.
-com calculates the com of the WHOLE first group!, not the com of the
molecules/residues of the first group;</SPAN></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: left; mso-pagination: widow-orphan; mso-char-indent-count: 1.0"
align=left><SPAN lang=EN-US
style="FONT-SIZE: 10pt; COLOR: black; FONT-FAMILY: Verdana; mso-font-kerning: 0pt; mso-bidi-font-family: 宋体">3.
Only when -nocom and -rdf atom are combined, the intramolecular exclusion is
considered;<o:p></o:p></SPAN></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: left; mso-pagination: widow-orphan; mso-char-indent-count: 1.0"
align=left><SPAN lang=EN-US
style="FONT-SIZE: 10pt; COLOR: black; FONT-FAMILY: Verdana; mso-font-kerning: 0pt; mso-bidi-font-family: 宋体">4.
RDF of multi-atoms/molecule(-nocom)---multi-atoms/molecule(-rdf mol_com) is
different from RDF of multi-atoms/molecule(-nocom)---single-atom/molecule(-rdf
atom), in which the single-atom is the center of the multi-atoms. Something
strange!!!<o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><B
style="mso-bidi-font-weight: normal"><SPAN lang=EN-US
style="FONT-SIZE: 10pt; COLOR: black; FONT-FAMILY: Verdana; mso-font-kerning: 0pt; mso-bidi-font-family: 宋体">Example:</SPAN></B><SPAN
lang=EN-US
style="FONT-SIZE: 10pt; COLOR: black; FONT-FAMILY: Verdana; mso-font-kerning: 0pt; mso-bidi-font-family: 宋体">
rdf[OAA_OAB_OAC_OAD(-nocom)---CAH_CAC_CAB(-rdf mol_com)] is quite different from
rdf[OAA_OAB_OAC_OAD (-nocom)---NAI(-rdf atom)], in which NAI is the center of
CAH_CAC_CAB.<o:p></o:p></SPAN></P><SPAN lang=EN-US
style="FONT-SIZE: 10pt; COLOR: black; FONT-FAMILY: Verdana; mso-font-kerning: 0pt; mso-bidi-font-family: 宋体">
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><BR></P></SPAN></FONT><FONT
face=Verdana size=2>From these results, it seems that there might be a
bug in the code. Or maybe there are some misunderstanding for me! If any
one has any suggestion about it, thanks in advance!</FONT></DIV>
<DIV><FONT face=Verdana size=2></FONT> </DIV>
<DIV><FONT face=Verdana size=2>regards,</FONT></DIV>
<DIV><FONT face=Verdana size=2>Baofu Qiao</FONT></DIV></BODY></HTML>