Sophie

Sophie

distrib > Fedora > 14 > x86_64 > media > updates > by-pkgid > 2f8321c8e2a11ea8b160a642cfc9fd7f > files > 195

towhee-doc-7.0.1-1.fc14.noarch.rpm

<html>
<head>
  <title>MCCCS Towhee (MM2)</title>
</head>

<body bgcolor="#FFFFFF" text="#000000">
<table width="675" border="0" cellspacing="0" cellpadding="0" height="590">
  <tr> 
    <td colspan="2" height="29"> 
      <div align="center"> <font size="5"> <b><font face="Arial, Helvetica, sans-serif"><a name="top"></a>MCCCS 
        Towhee (MM2)</font></b> </font> </div>
    </td>
  </tr>
<A href="http://sourceforge.net"> 
  <IMG src="http://sourceforge.net/sflogo.php?group_id=87039&amp;type=5" width="210" height="62" border="0" 
  alt="SourceForge.net Logo" align="right"/>
</A>
  <tr> 
    <td width="18" height="371" valign="top"> 
      <p>&nbsp; </p>
      <p>&nbsp;</p>
    </td>
    <td width="697" valign="top"> <b>Overview</b> 
      <ul>
        This section covers the MM2 force field as it is implemented into 
	the towhee_ff_MM2 file in the ForceFields directory.  This force field was originally 
	designed for to reproduce hydrocarbon crystal data.
	Note that this is an Exponential-6 force field that uses explicit mixing rules so it is
	not easily combined with other force fields.
	Any discrepencies (especially typos) from the published values are the sole responsibility
	of Marcus G. Martin, and I welcome feedback on how this implementation compares
	with other programs.
      </ul>

      <b>References for MM2</b> 
      <ul>
        MM2 is described in the following paper.
	<ul>
	  <li><a href="../references.html#allinger_1977">Allinger 1977</a></li>
	</ul>
      </ul>	

      <b>MM2 in Towhee</b> 
      <ul>
        The official force field name for MM2 in Towhee is 'MM2'.  Here I list all of 
	the atom names for use in the towhee_input file, along with a brief description.  I created these
	atom names in order to work with the molecule assembler.
	
	Please note that the capitalization and spacing pattern is important 
	and must be followed exactly as listed here.
	<ul>
          <li><b>'Ccc**(sp3)'</b> : Carbon single bonded to 2 or more other carbons.</li>
          <li><b>'Cchhh(sp3)'</b> : Carbon single bonded to 1 carbon and 3 hydrogens.</li>
          <li><b>'H'</b> : hydrogen.</li>
	</ul>
      </ul>
      <b>Coulombic interactions</b> 
      <ul>
        This force field does not use coulombic interactions.
      </ul>
      <a href="../towhee_capabilities.html">Return to the Towhee Capabilities web page</a> 
      <p>&nbsp;</p>
    </td>
  </tr>
</table>
<hr width="715" align="left">
<i><font size="2">Send comments to:</font></i> <font size="2"> 
<a href="mailto:marcus_martin@users.sourceforge.net">Marcus G. Martin</a><br>
<i>Last updated:</i> 
<!-- #BeginDate format:Am1 -->September 07, 2005<!-- #EndDate -->
</font> <br>
</body>
</html>