<html xmlns:v="urn:schemas-microsoft-com:vml" 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)">
<!--[if !mso]>
<style>
v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style>
<![endif]--><o:SmartTagType
namespaceuri="urn:schemas-microsoft-com:office:smarttags" name="State"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="place"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="City"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="PersonName"/>
<!--[if !mso]>
<style>
st1\:*{behavior:url(#default#ieooui) }
</style>
<![endif]-->
<style>
<!--
/* Font Definitions */
@font-face
        {font-family:Tahoma;
        panose-1:2 11 6 4 3 5 4 4 2 4;}
@font-face
        {font-family:-webkit-monospace;
        panose-1:0 0 0 0 0 0 0 0 0 0;}
/* 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:blue;
        text-decoration:underline;}
pre
        {margin:0in;
        margin-bottom:.0001pt;
        font-size:10.0pt;
        font-family:"Courier New";}
span.EmailStyle19
        {mso-style-type:personal-reply;
        font-family:Arial;
        color:navy;}
@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=blue>
<div class=Section1>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Dear Chansoo Kim,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>It has passed relatively long time since I
attempted to use pdb2gmx to build my topology for polyethylene. I prepared the
relevant files according to those used for amino acids. I used + and –
sign to discern the direction of connectivity. I have encountered dome problems
mentioned in the mail but they have not been answered satisfactorily. Later on
I wanted to run just united atom simulations and I had next problem with
pdb2gmx that always include hydrogen atoms to my topology though I used option
which should have disabled this. I decided to build my topology file without pdb2gmx
and I applied force field that is not present in GMX directories. <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<div>
<div class=MsoNormal align=center style='text-align:center'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=2 width="100%" align=center tabindex=-1>
</span></font></div>
<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'> gmx-users-bounces@gromacs.org
[mailto:gmx-users-bounces@gromacs.org] <b><span style='font-weight:bold'>On
Behalf Of </span></b>Chansoo Kim<br>
<b><span style='font-weight:bold'>Sent:</span></b> Tuesday, March 03, 2009 2:50
PM<br>
<b><span style='font-weight:bold'>To:</span></b> jalemkul@vt.edu; <st1:PersonName
w:st="on">Discussion list for GROMACS users</st1:PersonName><br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [gmx-users]
Polyethylene (PE) simulations in Gromacs - please!</span></font><o:p></o:p></p>
</div>
<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=3 face="Times New Roman"><span style='font-size:
12.0pt'>Dear Justin:<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Thank you for your reply.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>I was too urgent, so I did not clarify my questions.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Sorry about that.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>I totally understand how topology files (tdb, hdb, and etc..) work, but
I do not clearly understand chemical reaction, which I have to define in those
files...<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><span class=apple-style-span><b><font size=3 color=red
face="Times New Roman"><span style='font-size:12.0pt;color:red;font-weight:
bold'>[Situation]</span></font></b></span><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>I want to do simulate polyethylene (PE) using Gromacs and OPLS-AA force
field...<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><span class=apple-style-span><b><font size=3 color=red
face="Times New Roman"><span style='font-size:12.0pt;color:red;font-weight:
bold'>[Topology files and etc]</span></font></b></span><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><span class=apple-style-span><font size=3 color="#000099"
face="Times New Roman"><span style='font-size:12.0pt;color:#000099'> (1)
rtp file</span></font></span><o:p></o:p></p>
</div>
<div><pre><font size=2 face="Courier New"><span style='font-size:10.0pt'>[ Eth ]<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'> [ atoms ]<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'> C1 opls_136 -0.120 1<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'> H11 opls_140 0.060 1<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'> H12 opls_140 0.060 1<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'> C2 opls_136 -0.120 2<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'> H21 opls_140 0.060 2<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'> H22 opls_140 0.060 2<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'> [ bonds ]<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'> C1 H11<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'> C1 H12<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'> C1 C2<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'> C2 H21<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'> C2 H22<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'> C2 +C1<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><span
class=apple-style-span><font size=1 color="#000099" face=Arial><span
style='font-size:9.0pt;font-family:Arial;color:#000099'> (2) hdb file</span></font><font
color="#000099"><span style='color:#000099'><o:p></o:p></span></font></span></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Eth 2<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>2 6 H1 C1 C2 +C1<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>2 6 H2 C2 C1 -C2<o:p></o:p></span></font></pre>
<div>
<p class=MsoNormal><font size=3 face=-webkit-monospace><span style='font-size:
12.0pt;font-family:-webkit-monospace'><o:p> </o:p></span></font></p>
</div>
<div><pre><font size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><span
class=apple-style-span><font size=2 color="#000099" face=Arial><span
style='font-size:10.0pt;font-family:Arial;color:#000099'> (3) -c.tdb file</span></font></span><o:p></o:p></pre></div>
<div><pre><font size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>[ Eth ]<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>[ replace ]<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>C1 opls_135 12.011 -0.18<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>[ add ]<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>3 4 H1 C1 C2<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'> opls_140 1.008 0.06<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>[ delete ]<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>H21<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>H22<o:p></o:p></span></font></pre></div>
<div>
<p class=MsoNormal><font size=3 face=-webkit-monospace><span style='font-size:
12.0pt;font-family:-webkit-monospace'><o:p> </o:p></span></font></p>
</div>
<div><pre><font size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><span
class=apple-style-span><font size=2 color="#3333ff" face=Arial><span
style='font-size:10.0pt;font-family:Arial;color:#3333FF'> (4) -n.tdb file</span></font></span><o:p></o:p></pre></div>
</div>
<div><pre><font size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>[ Eth ]<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>[ replace ]<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>C2 opls_135 12.011 -0.18<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>[ add ]<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>3 4 H2 C2 C1<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'> opls_140 1.008 0.06<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>[ delete ]<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>H21<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>H22<o:p></o:p></span></font></pre></div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><span class=apple-style-span><font size=3 color="#000099"
face="Times New Roman"><span style='font-size:12.0pt;color:#000099'>
(5) input pdb file</span></font></span><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><span class=apple-style-span><font size=1
face=-webkit-monospace><span style='font-size:8.0pt;font-family:-webkit-monospace'>ATOM
1 C1 Eth 1 1.000 1.540 0.000</span></font></span><o:p></o:p></p>
</div>
<div><pre><font size=2 face="Courier New"><span style='font-size:10.0pt'>ATOM 2 C2 Eth 1 2.456 2.041 0.000<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>ATOM 3 C1 Eth 2 2.456 3.581 0.000<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>ATOM 4 C2 Eth 2 3.912 4.083 0.000<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>ATOM 5 C1 Eth 3 3.912 5.623 0.000<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>ATOM 6 C2 Eth 3 5.368 6.124 0.000<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>END<o:p></o:p></span></font></pre></div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><span class=apple-style-span><b><font size=3 color=red
face="Times New Roman"><span style='font-size:12.0pt;color:red;font-weight:
bold'>[Error]</span></font></b></span><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>When I did run the pdb2gmx, I got the following error.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>"Atom -C not found in residue PEth1 while adding hydrogens"<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><span class=apple-style-span><b><font size=3 color=red
face="Times New Roman"><span style='font-size:12.0pt;color:red;font-weight:
bold'>[Question #1 and #2]</span></font></b></span><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Therefore, what I should define more...?<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>What does the "+" and "-" mean here?<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><span class=apple-style-span><b><font size=3 color=red
face="Times New Roman"><span style='font-size:12.0pt;color:red;font-weight:
bold'>[If...]</span></font></b></span><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>If I change the hdb file as follows,<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div><pre><font size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Eth 2<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>2 6 H1 C1 C2 C1<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>2 6 H2 C2 C1 C2<o:p></o:p></span></font></pre></div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>After doing pdb2gmx, I got only 12 H-atoms (which means my terminal did
NOT work...).<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>And those positions are all (0, 0, 0).<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Following is the results,<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>LE Giving Russians Opium May Alter Current Situation<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>MODEL 1<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>ATOM 1 C1 PEt 1
1.000 0.000 0.000 1.00 0.00<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>ATOM 2 H11 PEt 1
0.000 0.000 0.000 1.00 0.00<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>ATOM 3 H12 PEt 1
0.000 0.000 0.000 1.00 0.00<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>ATOM 4 C2 PEt 1
2.450 6.000 1.000 1.00 0.00<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>ATOM 5 H21 PEt 1
0.000 0.000 0.000 1.00 0.00<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>ATOM 6 H22 PEt 1
0.000 0.000 0.000 1.00 0.00<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>ATOM 7 C1 PEt 2
2.450 6.000 1.000 1.00 0.00<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>ATOM 8 H11 PEt 2
0.000 0.000 0.000 1.00 0.00<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>ATOM 9 H12 PEt 2
0.000 0.000 0.000 1.00 0.00<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>ATOM 10 C2 PEt 2
3.910 2.000 3.000 1.00 0.00<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>ATOM 11 H21 PEt 2
0.000 0.000 0.000 1.00 0.00<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>ATOM 12 H22 PEt 2
0.000 0.000 0.000 1.00 0.00<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>ATOM 13 C1 PEt 3
3.910 2.000 3.000 1.00 0.00<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>ATOM 14 H11 PEt 3
0.000 0.000 0.000 1.00 0.00<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>ATOM 15 H12 PEt 3
0.000 0.000 0.000 1.00 0.00<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>ATOM 16 C2 PEt 3
5.360 8.000 4.000 1.00 0.00<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>ATOM 17 H21 PEt 3
0.000 0.000 0.000 1.00 0.00<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>ATOM 18 H22 PEt 3
0.000 0.000 0.000 1.00 0.00<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>TER<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>ENDMDL<o:p></o:p></span></font></p>
</div>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><span class=apple-style-span><b><font size=3 color=red
face="Times New Roman"><span style='font-size:12.0pt;color:red;font-weight:
bold'>[Question #3 from If... section ]</span></font></b></span><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>I guess that I have to change hdb and tdb files.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Would you please give some guide on that...?<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Thank you for your care!<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Sincerely yours,<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>C Kim<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>On Tue, Mar 3, 2009 at 8:35 AM, Justin A. Lemkul <<a
href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><br>
<br>
Chansoo Kim wrote:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Dear Dr. Benkova and others:<br>
<br>
<br>
I am C. Kim and trying to simulation polymer system.<br>
<br>
Since I guessed that polyethylene (PE) is a simple system, it could be not that
hard to simulate it in Gromacs.<br>
Trying to do, I have read Dr. Benkova's articles in gmx-users mailing list to
tackle my problems.<br>
Sorry to say, I could not solve problems, so I am asking your help!<br>
<br>
Actually I have used your files written in followings,<br>
<br>
<a href="http://www.mail-archive.com/gmx-users@gromacs.org/msg12204.html"
target="_blank">http://www.mail-archive.com/gmx-users@gromacs.org/msg12204.html</a><br>
<br>
[Q1]<br>
After getting the result from the pdb2gmx, I could not see any H-atoms in my
system.<br>
All the H-atoms have 0, 0, 0 positions!<br>
Therefore, my question is<br>
how I should define hdb?<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>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>The .hdb file format is explained in the manual.<o:p></o:p></span></font></p>
<div>
<blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;
margin-left:4.8pt;margin-right:0in'>
<p class=MsoNormal style='margin-bottom:12.0pt'><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=3 face="Times New Roman"><span style='font-size:
12.0pt'><br>
[Q2]<br>
When I use -C2, and +C1 in hdb file, I always meet error.<o:p></o:p></span></font></p>
</blockquote>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<p class=MsoNormal style='margin-bottom:12.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>What is the error?<br>
<br>
-Justin<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal style='margin-bottom:12.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>Is there any other things
to add to the ffopls*.* files...?<br>
<br>
Thank you for your care!<br>
<br>
<br>
Sincerely <br>
C. Kim<br>
<br>
<o:p></o:p></span></font></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>------------------------------------------------------------------------<br>
<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org"
target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search"
target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or
send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php"
target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
<st1:place w:st="on"><st1:City w:st="on">Blacksburg</st1:City>, <st1:State
w:st="on">VA</st1:State></st1:place><br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org"
target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search"
target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or
send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php"
target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><o:p></o:p></span></font></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
</div>
</body>
</html>