Sophie

Sophie

distrib > Fedora > 18 > i386 > by-pkgid > 01fdc0b336185a24a094689dccd5b064 > files > 212

towhee-doc-7.0.4-2.fc18.noarch.rpm

<html>
<head>
  <title>MCCCS Towhee (SKS)</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 (SKS)</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 Smit-Karaborni-Siepmann Force Field (SKS) for n-alkanes as it is implemented 
	into the towhee_ff_SKS file in the ForceFields directory. All of the Towhee atom types for this force field 
        are listed, along with a short description of their meanings.
        SKS uses a 'Lennard-Jones' classical_potential and the 'Lorentz-Berthelot' classical_mixrule.
	This forcefield is best used with a 13.8 Angstrom cutoff with no tail corrections and without shifting 
	at the cutoff.  This strange set of parameters is due to a bug in the code originally used to produce 
	this forcefield.  Please see the Erratum in the references section for more information.
	The SKS forcefield was later extended to branched alkanes (<a href="smmkmain.html">SMMK Main</a>) 
	and eventually replaced by the <a href="trappeua.html">TraPPE-UA</a> force field.
        Any discrepencies (especially typos) from the published force field 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 SKS</b> 
      <ul>
        The parameters and detailed results for the SKS force field are found here.
        <ul>
          <li><a href="../references.html#smit_et_al_1995">Smit <i>et al.</i> 1995</a></li>
        </ul>
	Please note that an error was made in the code that produced the results in that paper that 
	essentially meant that tail corrections were not employed.  Please see the following erratum
	for more information.
        <ul>
          <li><a href="../references.html#smit_et_al_erratum_1998">Smit <i>et al.</i> Erratum 1998</a></li>
        </ul>
      </ul>
      <b>SKS in Towhee</b> 
      <ul>
        The official force field name for SKS in Towhee is 'SKS'. Here 
        I list all of the atom names for use in the towhee_input file, 
        along with a brief description.
	Please note that the capitalization and spacing pattern is important and must be followed exactly 
	as listed here. 
        <ul>
          <li><b>'CH3'</b> methyl group (C plus 3 bonded H as a united-atom) on an <i>n</i>-alkane of C<sub>4</sub> or longer.</li>
          <li><b>'CH2'</b> methylene group (C plus 2 bonded H as a united-atom) on an <i>n</i>-alkane of C<sub>4</sub> or longer.</li>
        </ul>
      </ul>
      <b>Coulombic interactions</b> 
      <ul>
        There are no coulombic interactions for this force field.
      </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>