Sophie

Sophie

distrib > Fedora > 14 > x86_64 > media > updates > by-pkgid > 2f8321c8e2a11ea8b160a642cfc9fd7f > files > 212

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

<html>
<head>
  <title>MCCCS Towhee (Smith and Dang 1994)</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 (Smith and Dang 1994)</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 Smith and Dang 1994 non-polarizable parameters for NaCl in SPC/E water as 
	they are implemented into the towhee_ff_Smith1994 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.
	Note that this is a Lennard-Jones (12-6) force fields that use Geometric mixing rules and can only 
	be combined with other Lennard-Jones (12-6) force fields.  It was designed to be used in combination 
	with the <a href="spce.html">SPC/E</a> water model.
        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 Smith and Dang 1994</b> 
      <ul>
	<ul>
	  <li><a href="../references.html#smith_dang_1994">Smith and Dang 1994</a></li>
	</ul>
      </ul>	
      <b>Smith and Dang 1994 in Towhee</b> 
      <ul>
        The official force field name for Smith and Dang 1994 in Towhee is 'Smith1994'.  Here I list all of 
	the atom names for use in the towhee_input file, along with a brief description.  The meanings should 
	be quite obvious for this force field.
	Please note that the capitalization and spacing pattern is important 
	and must be followed exactly as listed here.
	<ul>
	  <li><b>'Na'</b> : sodium ion with a +1 charge.</li>
	  <li><b>'Cl'</b> : chloride ion with a -1 charge.</li>
	</ul>
      </ul>
      <b>Coulombic interactions</b> 
      <ul>
        This force field uses atom-centered point charges to represent the electrostatic interactions.
	The 'bond increment' method for assigning charges is implemented for these molecules.
	Please see the <a href="../inpstyle/inpstyle_2.html">inpstyle 2</a> documentation for 
	further information on enabling this option.  As there are no bonds this option will simply 
	assign the default ionic charges of +1 to sodium and -1 to chloride.
      </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>