<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta http-equiv=Content-Type content="text/html; charset=us-ascii">
<meta name=Generator content="Microsoft Word 10 (filtered)">
<style>
<!--
/* Font Definitions */
@font-face
{font-family:Courier;
panose-1:2 7 4 9 2 2 5 2 4 4;}
@font-face
{font-family:SimSun;
panose-1:2 1 6 0 3 1 1 1 1 1;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
@font-face
{font-family:"\@SimSun";
panose-1:2 1 6 0 3 1 1 1 1 1;}
@font-face
{font-family:CMR8;
panose-1:0 0 0 0 0 0 0 0 0 0;}
@font-face
{font-family:CMMI10;
panose-1:0 0 0 0 0 0 0 0 0 0;}
@font-face
{font-family:CMR10;
panose-1:0 0 0 0 0 0 0 0 0 0;}
@font-face
{font-family:CMSY8;
panose-1:0 0 0 0 0 0 0 0 0 0;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman";
color:black;}
a:link, span.MsoHyperlink
{color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{color:blue;
text-decoration:underline;}
pre
{margin:0cm;
margin-bottom:.0001pt;
font-size:10.0pt;
font-family:"Courier New";
color:black;}
span.EmailStyle18
{font-family:Arial;
color:navy;}
@page Section1
{size:612.0pt 792.0pt;
margin:72.0pt 90.0pt 72.0pt 90.0pt;}
div.Section1
{page:Section1;}
-->
</style>
</head>
<body bgcolor=white lang=EN-US link=blue vlink=blue>
<div class=Section1>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=black
face="Times New Roman"><span style='font-size:11.0pt;color:windowtext'>Dear Yangye
and Gromacs users</span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=black
face="Times New Roman"><span style='font-size:11.0pt;color:windowtext'> </span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=black
face="Times New Roman"><span style='font-size:11.0pt;color:windowtext'>On page
125 of manual-3.2.pdf, it is stated that table.xvg has seven</span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=black
face="Times New Roman"><span style='font-size:11.0pt;color:windowtext'>columns
of table lookup data in the order: </span></font><font size=2 color=black
face=CMMI10><span style='font-size:11.0pt;font-family:CMMI10;color:windowtext'>x</span></font><font
size=2 color=black><span style='font-size:11.0pt;color:windowtext'>, </span></font><font
size=2 color=black face=CMMI10><span style='font-size:11.0pt;font-family:CMMI10;
color:windowtext'>f</span></font><font size=2 color=black face=CMR10><span
style='font-size:11.0pt;font-family:CMR10;color:windowtext'>(</span></font><font
size=2 color=black face=CMMI10><span style='font-size:11.0pt;font-family:CMMI10;
color:windowtext'>x</span></font><font size=2 color=black face=CMR10><span
style='font-size:11.0pt;font-family:CMR10;color:windowtext'>)</span></font><font
size=2 color=black><span style='font-size:11.0pt;color:windowtext'>, </span></font><font
size=2 color=black face=CMMI10><span style='font-size:11.0pt;font-family:CMMI10;
color:windowtext'>f</span></font><font size=1 color=black face=CMSY8><span
style='font-size:8.0pt;font-family:CMSY8;color:windowtext'>^(2)</span></font><font
size=2 color=black face=CMR10><span style='font-size:11.0pt;font-family:CMR10;
color:windowtext'>(</span></font><font size=2 color=black face=CMMI10><span
style='font-size:11.0pt;font-family:CMMI10;color:windowtext'>x</span></font><font
size=2 color=black face=CMR10><span style='font-size:11.0pt;font-family:CMR10;
color:windowtext'>)</span></font><font size=2 color=black><span
style='font-size:11.0pt;color:windowtext'>, </span></font><font size=2
color=black face=CMMI10><span style='font-size:11.0pt;font-family:CMMI10;
color:windowtext'>g</span></font><font size=2 color=black face=CMR10><span
style='font-size:11.0pt;font-family:CMR10;color:windowtext'>(</span></font><font
size=2 color=black face=CMMI10><span style='font-size:11.0pt;font-family:CMMI10;
color:windowtext'>x</span></font><font size=2 color=black face=CMR10><span
style='font-size:11.0pt;font-family:CMR10;color:windowtext'>)</span></font><font
size=2 color=black><span style='font-size:11.0pt;color:windowtext'>, </span></font><font
size=2 color=black face=CMMI10><span style='font-size:11.0pt;font-family:CMMI10;
color:windowtext'>g</span></font><font size=1 color=black face=CMSY8><span
style='font-size:8.0pt;font-family:CMSY8;color:windowtext'>^(2)</span></font><font
size=2 color=black face=CMR10><span style='font-size:11.0pt;font-family:CMR10;
color:windowtext'>(</span></font><font size=2 color=black face=CMMI10><span
style='font-size:11.0pt;font-family:CMMI10;color:windowtext'>x</span></font><font
size=2 color=black face=CMR10><span style='font-size:11.0pt;font-family:CMR10;
color:windowtext'>)</span></font><font size=2 color=black><span
style='font-size:11.0pt;color:windowtext'>, </span></font><font size=2
color=black face=CMMI10><span style='font-size:11.0pt;font-family:CMMI10;
color:windowtext'>h</span></font><font size=2 color=black face=CMR10><span
style='font-size:11.0pt;font-family:CMR10;color:windowtext'>(</span></font><font
size=2 color=black face=CMMI10><span style='font-size:11.0pt;font-family:CMMI10;
color:windowtext'>x</span></font><font size=2 color=black face=CMR10><span
style='font-size:11.0pt;font-family:CMR10;color:windowtext'>)</span></font><font
size=2 color=black><span style='font-size:11.0pt;color:windowtext'>, </span></font><font
size=2 color=black face=CMMI10><span style='font-size:11.0pt;font-family:CMMI10;
color:windowtext'>h</span></font><font size=1 color=black face=CMSY8><span
style='font-size:8.0pt;font-family:CMSY8;color:windowtext'>^(2)</span></font><font
size=2 color=black face=CMR10><span style='font-size:11.0pt;font-family:CMR10;
color:windowtext'>(</span></font><font size=2 color=black face=CMMI10><span
style='font-size:11.0pt;font-family:CMMI10;color:windowtext'>x</span></font><font
size=2 color=black face=CMR10><span style='font-size:11.0pt;font-family:CMR10;
color:windowtext'>)</span></font><font size=2 color=black><span
style='font-size:11.0pt;color:windowtext'>, but on page 134, it is mentioned
that this file should contain 7 columns: the </span></font><font size=2
color=black face=Courier><span style='font-size:11.0pt;font-family:Courier;
color:windowtext'>x</span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=black
face="Times New Roman"><span style='font-size:11.0pt;color:windowtext'>, </span></font><font
size=2 color=black face=Courier><span style='font-size:11.0pt;font-family:Courier;
color:windowtext'>f(x)</span></font><font size=2 color=black><span
style='font-size:11.0pt;color:windowtext'>, </span></font><font size=2
color=black face=Courier><span style='font-size:11.0pt;font-family:Courier;
color:windowtext'>-f^</span></font><font size=1 color=black face=CMR8><span
style='font-size:8.0pt;font-family:CMR8;color:windowtext'>(2)</span></font><font
size=2 color=black face=Courier><span style='font-size:11.0pt;font-family:Courier;
color:windowtext'>(x)</span></font><font size=2 color=black><span
style='font-size:11.0pt;color:windowtext'>, </span></font><font size=2
color=black face=Courier><span style='font-size:11.0pt;font-family:Courier;
color:windowtext'>g(x)</span></font><font size=2 color=black><span
style='font-size:11.0pt;color:windowtext'>, </span></font><font size=2
color=black face=Courier><span style='font-size:11.0pt;font-family:Courier;
color:windowtext'>-g^</span></font><font size=1 color=black face=CMR8><span
style='font-size:8.0pt;font-family:CMR8;color:windowtext'>(2)</span></font><font
size=2 color=black face=Courier><span style='font-size:11.0pt;font-family:Courier;
color:windowtext'>(x)</span></font><font size=2 color=black><span
style='font-size:11.0pt;color:windowtext'>, </span></font><font size=2
color=black face=Courier><span style='font-size:11.0pt;font-family:Courier;
color:windowtext'>h(x)</span></font><font size=2 color=black><span
style='font-size:11.0pt;color:windowtext'>, </span></font><font size=2
color=black face=Courier><span style='font-size:11.0pt;font-family:Courier;
color:windowtext'>-h^</span></font><font size=1 color=black face=CMR8><span
style='font-size:8.0pt;font-family:CMR8;color:windowtext'>(2)</span></font><font
size=2 color=black face=Courier><span style='font-size:11.0pt;font-family:Courier;
color:windowtext'>(x)</span></font><font size=2 color=black><span
style='font-size:11.0pt;color:windowtext'>. Can you please let know which one
is correct?</span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=black
face="Times New Roman"><span style='font-size:11.0pt;color:windowtext'> </span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=black
face="Times New Roman"><span style='font-size:11.0pt;color:windowtext'>Happy
new year to you all,</span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=black
face="Times New Roman"><span style='font-size:11.0pt;color:windowtext'> </span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=black
face="Times New Roman"><span style='font-size:11.0pt;color:windowtext'>Junfang</span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=black
face="Times New Roman"><span style='font-size:10.0pt;color:windowtext'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal style='margin-left:36.0pt'><font size=2 color=black
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma;color:windowtext'>-----Original
Message-----<br>
<b><span style='font-weight:bold'>From:</span></b>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b><span
style='font-weight:bold'>On Behalf Of </span></b>Yang Ye<br>
<b><span style='font-weight:bold'>Sent:</span></b> </span></font><font size=2 color=black face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma;
color:windowtext'>Thursday, 22 December 2005</span></font><font size=2
color=black face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma;
color:windowtext'> </span></font><font size=2 color=black face=Tahoma><span
style='font-size:10.0pt;font-family:Tahoma;color:windowtext'>6:10 PM</span></font><font
size=2 color=black face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma;
color:windowtext'><br>
<b><span style='font-weight:bold'>To:</span></b> Discussion list for GROMACS
users<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [gmx-users]</span></font></p>
<p class=MsoNormal style='margin-left:36.0pt'><font size=3 color=black
face="Times New Roman"><span style='font-size:12.0pt'> </span></font></p>
<p class=MsoNormal style='margin-left:36.0pt'><font size=3 color=black
face="Times New Roman"><span style='font-size:12.0pt'>Try use table (see manual
6.4.2). Note that there is new option available in 3.3 that you can assign
different table for the interactions between different groups of atoms. Check
3.3's document (share/html/online.html), section "mdp option".<br>
<br>
Yang Ye<br>
<br>
<a href="mailto:Junfang.Zhang@csiro.au">Junfang.Zhang@csiro.au</a> wrote: </span></font></p>
<pre style='margin-left:36.0pt' wrap=""><font size=2 color=black
face="Courier New"><span style='font-size:10.0pt'>Dear Gromacs users,</span></font></pre><pre
style='margin-left:36.0pt'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'> </span></font></pre><pre style='margin-left:
36.0pt'><font size=2 color=black face="Courier New"><span style='font-size:
10.0pt'>If I use the MCY potential which takes the form as follows</span></font></pre><pre
style='margin-left:36.0pt'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'>(a exp (-br) - c exp (-dr) + qq/r),</span></font></pre><pre
style='margin-left:36.0pt'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'> </span></font></pre><pre style='margin-left:
36.0pt'><font size=2 color=black face="Courier New"><span style='font-size:
10.0pt'>which source files in GROMACS do I need to modify?</span></font></pre><pre
style='margin-left:36.0pt'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'> </span></font></pre><pre style='margin-left:
36.0pt'><font size=2 color=black face="Courier New"><span style='font-size:
10.0pt'> </span></font></pre><pre style='margin-left:36.0pt'><font size=2
color=black face="Courier New"><span style='font-size:10.0pt'>Thanks,</span></font></pre><pre
style='margin-left:36.0pt'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'> </span></font></pre><pre style='margin-left:
36.0pt'><font size=2 color=black face="Courier New"><span style='font-size:
10.0pt'>Junfang</span></font></pre><pre style='margin-left:36.0pt'><font
size=2 color=black face="Courier New"><span style='font-size:10.0pt'> </span></font></pre><pre
style='margin-left:36.0pt'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'>_______________________________________________</span></font></pre><pre
style='margin-left:36.0pt'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'>gmx-users mailing list</span></font></pre><pre
style='margin-left:36.0pt'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a></span></font></pre><pre
style='margin-left:36.0pt'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'><a
href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a></span></font></pre><pre
style='margin-left:36.0pt'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'>Please don't post (un)subscribe requests to the list. Use the </span></font></pre><pre
style='margin-left:36.0pt'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'>www interface or send it to <a
href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.</span></font></pre><pre
style='margin-left:36.0pt'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'> </span></font></pre><pre style='margin-left:
36.0pt'><font size=2 color=black face="Courier New"><span style='font-size:
10.0pt'> </span></font></pre>
<p class=MsoNormal style='margin-left:36.0pt'><font size=3 color=black
face="Times New Roman"><span style='font-size:12.0pt'> </span></font></p>
<div>
<p class=MsoNormal style='margin-left:36.0pt'><font size=3 color=black
face="Times New Roman"><span style='font-size:12.0pt'>-- <br>
<i><span style='font-style:italic'>Regards,</span></i><br>
Yang Ye<br>
</span></font><i><font size=2><span style='font-size:10.0pt;font-style:italic'>Computational
Biology Lab<br>
</span></font></i><i><font size=2><span style='font-size:10.0pt;font-style:
italic'>School</span></font></i><i><font size=2><span style='font-size:10.0pt;
font-style:italic'> of </span></font></i><i><font size=2><span
style='font-size:10.0pt;font-style:italic'>Biological</span></font></i><i><font
size=2><span style='font-size:10.0pt;font-style:italic'> Sciences<br>
Nanyang Technological University<br>
</span></font></i><i><font size=2><span style='font-size:10.0pt;font-style:
italic'>Singapore</span></font></i><i><font size=2><span style='font-size:
10.0pt;font-style:italic'><br>
Tel: 6316-2884</span></font></i></p>
</div>
</div>
</body>
</html>