Sophie

Sophie

distrib > Fedora > 14 > x86_64 > media > updates > by-pkgid > 2f8321c8e2a11ea8b160a642cfc9fd7f > files > 192

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

<html>
 <head>
  <title>MCCCS Towhee (MCY1976)</title>
 </head>

 <body bgcolor="#FFFFFF" text="#000000">
  <table width="800" 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 (MCY1976)</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="700" valign="top"> <b>Overview</b> 
     <ul>
      This section covers the MCY1976 force field that has two similar four-site water models.  This forcefield is implemented into the towhee_ff_MCY1976
      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.
      MCY1976 has two different rigid water models with 'Double Exponential' terms on the hydrogens and oxygens and charge sites on the hydrogens and along
      the bisector between the hydrogens.  These are branched, rigid molecules (when you consider the charged interaction site) and it is recommended to 
      generate initial structures from a template and also to use the rotational-bias moves instead of the configurational-bias moves for molecule transfers
      between simulation boxes.
      Any discrepencies (especially typos) from the published force field values are the sole responsibility of 
      <a href="mailto:marcus_martin@users.sourceforge.net">Marcus Martin</a>, and we welcome feedback on how this implementation compares with other programs. 
      <p>&nbsp;</p>
     </ul>

     <b>References for MCY1976</b> 
     <ul>
      MCY1976 was originally published in the following paper
      <ul>
       <li><a href="../references.html#matsuoka_et_al_1976">Matsuoka <i>et al.</i> 1976</a></li>
      </ul>
     </ul>
 
     <b>MCY1976 in Towhee</b> 
     <ul>
      The official force field name for this potential in Towhee is 'MCY1976'.  This section lists all of the atom names for use in the towhee_input file, 
      along with a brief description of the atom names.
      Please note that the capitalization and spacing pattern is important and must be followed exactly as listed here. 
      <ul>
       <li><b>'H:CI'</b> : hydrogen in water using the model they fit to the CI data</li>
       <li><b>'O:CI'</b> : oxygen in water using the model they fit to the CI data</li>
       <li><b>'M:CI'</b> : charge site along the bisector between the hydrogens using the model they fit to the CI data</li>
       <li><b>'H:inter'</b> : hydrogen in water using the model they fit to the inter data</li>
       <li><b>'O:inter'</b> : oxygen in water using the model they fit to the inter data</li>
       <li><b>'M:inter'</b> : charge site along the bisector between the hydrogens using the model they fit to the inter data</li>
      </ul>
     </ul>

     <b>Coulombic interactions</b> 
     <ul>
      This forcefield uses atom-centered point charges to represent the electrostatic interactions.
      The 'bond increment' method is implemented for this potential and assigns charges according to Table VIII of their original paper.
     </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"></hr>
  <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></br>
   <i>Last updated:</i> <!-- #BeginDate format:Am1 -->January 05, 2007<!-- #EndDate -->
  </font>
  <br></br>
 </body>
</html>