<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:m="http://schemas.microsoft.com/office/2004/12/omml" 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 12 (filtered medium)">
<style>
<!--
/* Font Definitions */
@font-face
{font-family:Helvetica;
panose-1:2 11 6 4 2 2 2 2 2 4;}
@font-face
{font-family:Helvetica;
panose-1:2 11 6 4 2 2 2 2 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
@font-face
{font-family:Times;
panose-1:2 2 6 3 5 4 5 2 3 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.apple-style-span
{mso-style-name:apple-style-span;}
span.yshortcuts
{mso-style-name:yshortcuts;}
span.EmailStyle19
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
-->
</style>
<!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang=EN-US link=blue vlink=purple>
<div class=WordSection1>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Check the original specifications for each of those force
fields, then check to see if the molecule you are wanting to simulate falls
within the boundaries of how the force field was derived. Also search the
literature for simulations of the same or similar molecules, and see which
force fields they used.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<div>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Catch ya,<br>
<br>
Dr. Dallas Warren<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Medicinal Chemistry and Drug Action<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Monash Institute of Pharmaceutical Sciences</span><span
style='font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>,
Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
dallas.warren@monash.edu<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>+61 3 9903 9304<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a
nail.</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'> <o:p></o:p></span></p>
</div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<div style='border:none;border-left:solid blue 1.5pt;padding:0cm 0cm 0cm 4.0pt'>
<div>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b>On
Behalf Of </b>Sanku M<br>
<b>Sent:</b> Thursday, 28 October 2010 6:06 AM<br>
<b>To:</b> gmx-users@gromacs.org<br>
<b>Subject:</b> [gmx-users] United atom forcefield for long alkane ?<o:p></o:p></span></p>
</div>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<div>
<div>
<div>
<p class=MsoNormal><span style='font-family:"Times","serif"'>Hi,<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-family:"Times","serif"'> I was
planning to simulate a system of long-chain alkane carboxylate in water
with a <span class=yshortcuts>chemical formula</span> CH3-(CH2)_20-COOH
.<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-family:"Times","serif"'>For that I was
thinking of using an united atom force-field. I found , in gromacs, there are
two United atom force-field available: GROMOS-96 and OPLS-UA. I was wondering
whether some one can suggest which united atom force-field will be good choice
for such a long chain alkane chain ?<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-family:"Times","serif"'>Thanks<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-family:"Times","serif"'>Sanku<o:p></o:p></span></p>
</div>
</div>
</div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
</div>
</body>
</html>