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

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  <title>MCCCS Towhee (Morrow2002)</title>
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      <div align="center"> <font size="5"> <b><font face="Arial, Helvetica, sans-serif"><a name="top"></a>MCCCS 
        Towhee (Morrow and Maginn 2002)</font></b> </font> </div>
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      <p>&nbsp; </p>
      <p>&nbsp;</p>
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    <td width="697" valign="top"> <b>Overview</b> 
      <ul>
        This section covers the Morrow and Maginn 2002 (Morrow2002) force field as it is implemented into 
	the towhee_ff_Morrow2002 file in the ForceFields directory.  This force field was
	designed for an ionic liquid of 1-<i>n</i>-butyl-3-methylimidazolium [bmim] hexafluorophosphate [PF<sub>6</sub>].
	Note that this is a Lennard-Jones force field that uses the 'Lorentz-Berthelot' mixing rules.
	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 Morrow and Maginn 2002</b> 
      <ul>
        This forcefield is described in a single paper and an erratum.
	<ul>
	  <li><a href="../references.html#morrow_maginn_2002">Morrow and Maginn 2002</a></li>
	  <li><a href="../references.html#morrow_maginn_2003">Morrow and Maginn 2003</a> erratum</li>
	</ul>
      </ul>	

      <b>Typos and comments for Morrow and Maginn 2002</b>
      <ul>
        <li>The parameters implemented for this force field are from the erratum.</li>
	<li>All bonds involving hydrogen were held rigid in their work using SHAKE, and are therefore implemented here as rigid bonds.</li>
	<li>Full Lennard-Jones interactions are used for 1-4 interactions, while the Coulombic 1-4 terms are scaled by 1/2 
	  [personal communication between E.J. Maginn and M.G. Martin 04-21-2006].
	</li>
	<li>The second to last angle term in Table 2 of the erratum should read N-C<sub>7</sub>-H<sub>7,8</sub> instead of 
	  N-C<sub>7</sub>-H<sub>8,9</sub> [personal communication between E.J. Maginn and M.G. Martin 04-21-2006].
	</li>
	<li>No value for the H-C8-C9-H dihedral was specified in their papers.  It has been implemented here using the published 
	  H-C7-C8-H term.
	</li>
	<li>The authors claim that the charge on PF<sub>6</sub> adds up to -0.904, and the charge on bmim adds up to 0.904.  However, 
	  the partial charges they list for PF<sub>6</sub> using assymmetric charge assignments adds up to -0.903, which does not properly 
	  balance the charge of the bmin.  I have adjusted this by utlizing the stated charges on the Fluorines, and placing the remainder of 
	  the charge on the Phosphorous.
      </ul>

      <b>Morrow and Maginn 2002 in Towhee</b> 
      <ul>
        The official force field name for Morrow and Maginn 2002 in Towhee is 'Morrow2002'.  Here is the list
	of atom names for use in the towhee_input file, along with a brief description.  These names correspond to those 
	used in <a href="../references.html#morrow_maginn_2002">Morrow and Maginn 2002</a>.
	Please note that the capitalization and spacing pattern is important 
	and must be followed exactly as listed here.
	<ul>
          <li><b>'N1'</b> : Ring Nitrogen bonded to C2, C5, and C7 in bmim</li>
          <li><b>'C2'</b> : Ring Carbon bonded to N1, N3, and H1 in bmim</li>
          <li><b>'N3'</b> : Ring Nitrogen bonded to C2, C4, and C6 in bmim</li>
          <li><b>'C4'</b> : Ring Carbon bonded to N3, C5, and H2 in bmim</li>
          <li><b>'C5'</b> : Ring Carbon bonded to N1, C4, and H3 in bmim</li>
          <li><b>'C6'</b> : methyl Carbon bonded to N3, H4, H5, and H6 in bmim</li>
          <li><b>'C7'</b> : methylene Carbon bonded to N1, C8, H7, and H8 in bmim</li>
          <li><b>'C8'</b> : methylene Carbon bonded to C7, C9, H9, and H10 in bmim</li>
          <li><b>'C9'</b> : methylene Carbon bonded to C8, C10, H11, and H12 in bmim</li>
          <li><b>'C10'</b> : methyl Carbon bonded to C9, H13, H14, and H15 in bmim</li>
          <li><b>'H1'</b> : Hydrogen bonded to C2 in bmim</li>
          <li><b>'H2'</b> : Hydrogen bonded to C4 in bmim</li>
          <li><b>'H3'</b> : Hydrogen bonded to C5 in bmim</li>
          <li><b>'H4'</b> : Hydrogen bonded to C6 in bmim</li>
          <li><b>'H5'</b> : Hydrogen bonded to C6 in bmim</li>
          <li><b>'H6'</b> : Hydrogen bonded to C6 in bmim</li>
          <li><b>'H7'</b> : Hydrogen bonded to C7 in bmim</li>
          <li><b>'H8'</b> : Hydrogen bonded to C7 in bmim</li>
          <li><b>'H9'</b> : Hydrogen bonded to C8 in bmim</li>
          <li><b>'H10'</b> : Hydrogen bonded to C8 in bmim</li>
          <li><b>'H11'</b> : Hydrogen bonded to C9 in bmim</li>
          <li><b>'H12'</b> : Hydrogen bonded to C9 in bmim</li>
          <li><b>'H13'</b> : Hydrogen bonded to C10 in bmim</li>
          <li><b>'H14'</b> : Hydrogen bonded to C10 in bmim</li>
          <li><b>'H15'</b> : Hydrogen bonded to C10 in bmim</li>
          <li><b>'P'</b> : P in hexafluorophosphate</li>
          <li><b>'F'</b> : generic F in hexafluorophosphate if you want to use the symmetric charge distribution 
	    version of that molecule.
	  </li>
          <li><b>'F1'</b> : specific F in hexafluorophosphate if you want to use the assymmetric charge distribution 
	    version of that molecule.
	  </li>
          <li><b>'F2'</b> : specific F in hexafluorophosphate if you want to use the assymmetric charge distribution 
	    version of that molecule.
	  </li>
          <li><b>'F3'</b> : specific F in hexafluorophosphate if you want to use the assymmetric charge distribution 
	    version of that molecule.
	  </li>
          <li><b>'F4'</b> : specific F in hexafluorophosphate if you want to use the assymmetric charge distribution 
	    version of that molecule.
	  </li>
          <li><b>'F5'</b> : specific F in hexafluorophosphate if you want to use the assymmetric charge distribution 
	    version of that molecule.
	  </li>
          <li><b>'F6'</b> : specific F in hexafluorophosphate if you want to use the assymmetric charge distribution 
	    version of that molecule.
	  </li>
	</ul>
      </ul>
      <b>Coulombic interactions</b> 
      <ul>
        This force field uses point charges and has been set up to assign the point charges using the bond increment method.
	The charges for bmim are assigned according to Table 1 of 
	<a href="../references.html#morrow_maginn_2002">Morrow and Maginn 2002</a>.
	There are two possible charge distributions for hexafluorophosphate.  If you specify each of the Fluorine atoms (F1, ..., F6) 
	then the charges are assigned according to Table 1 of
	<a href="../references.html#morrow_maginn_2002">Morrow and Maginn 2002</a>, with the exception that the P charge is 1.457 instead 
	of the stated 1.478 (see the notes above).  If you specify a generic Fluorine atom (F), then
	the charge on the Phosphorous is the same as in Table 1, while the Fluorines are assigned symmetric charges in order to achieve 
	a total molecule charge of -0.904.
      </ul>
      <a href="../towhee_capabilities.html">Return to the Towhee Capabilities web page</a> 
      <p>&nbsp;</p>
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<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 -->April 24, 2006<!-- #EndDate -->
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