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<title>MCCCS Towhee (Dubb2004)</title>
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<div align="center"> <font size="5"> <b><font face="Arial, Helvetica, sans-serif"><a name="top"></a>MCCCS
Towhee (Dubbeldam <i>et al.</i> 2004)</font></b> </font> </div>
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<td width="697" valign="top"> <b>Overview</b>
<ul>
This section covers the Dubbeldam <i>et al.</i> (Dubb2004) force field as it is implemented into
the towhee_ff_Dubb2004 file in the ForceFields directory. This force field is for adsorption
simulations of alkanes in various Zeolites.
Note that this is a Lennard-Jones 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.
<p> </p>
</ul>
<b>References for Dubb2004</b>
<ul>
What I term Dubb2004 is described in several papers.
<ul>
<li><a href="../references.html#dubbeldam_et_al_2004_prl">Dubbeldam <i>et al.</i> 2004 PRL</a></li>
<li><a href="../references.html#dubbeldam_et_al_2004_jpcb">Dubbeldam <i>et al.</i> 2004 JPCB</a></li>
<li><a href="../references.html#calero_et_al_2004">Calero <i>et al.</i> 2004</a></li>
</ul>
In addition, some of their torsional interactions are overly complicated. The torsions
involving the <b>CH</b> group are specified in terms of where the hydrogen would be if it was explicitly
included in the simulation. Thijs Vlugt suggested replacing the torsions involving the <b>CH</b> group
with those from the TraPPE-UA forcefield and I have followed that suggestion for this implementation.
</ul>
<b>Dubb2004 in Towhee</b>
<ul>
The official force field name for Dubbeldam <i>et al.</i> United Atom in Towhee is 'Dubb2004'. 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. Dubb2004 is a united-atom force field which lumps
hydrogens onto their neighboring carbons. It is also designed for work with Silaceous and aluminum substituted
zeolites. The general pattern of the names is a list of the atoms that
make up the group, followed by the hybridization of the central atom, and ending in a character string that
distinguishes similar atoms.
Please note that the capitalization and spacing pattern is important
and must be followed exactly as listed here.
<ul>
<dt><font color="red">sp<sup>3</sup> hybridized Carbons</font></dt>
<li><b>'CH4'</b> : sp<sup>3</sup> carbon plus the 4 hydrogens bonded to it (united-atom) in methane.</li>
<li><b>'CH3'</b> : sp<sup>3</sup> carbon plus the 3 hydrogens bonded to it (united-atom) in ethane.</li>
<li><b>'CH2'</b> : sp<sup>3</sup> carbon plus the 2 hydrogens bonded to it (united-atom).</li>
<li><b>'CH'</b> : sp<sup>3</sup> carbon plus the 1 hydrogen bonded to it (united-atom).</li>
<li><b>'C'</b> : sp<sup>3</sup> carbon that is not bonded to any hydrogens.</li>
<dt><font color="red">Zeolite Framework Atoms</font></dt>
<li><b>'O'</b> : oxygen bonded to silicon and/or aluminum in the zeolite framework.</li>
<li><b>'Si'</b> : silicon bonded to four oxygens in the zeolite framework.</li>
<li><b>'Al'</b> : aluminum bonded to four oxygens in the zeolite framework.</li>
<dt><font color="red">Zeolite Counter Ions</font></dt>
<li><b>'Na'</b> : sodium ion.</li>
</ul>
</ul>
<b>Coulombic interactions</b>
<ul>
There are specific charge assignents for the atoms in the zeolite framework and these assignments are enforced
by the angle potential for the zeolite. There are no charges on the alkane united-atoms. The 'bond increment'
method of <b>charge_assignment</b> is implemented for this forcefield.
Please see the <a href="../inpstyle/inpstyle_2.html">inpstyle 2</a> documentation for
further information on enabling this option. Otherwise, you are welcome to manually set the charges. Here I
list the charges that are assigned by the 'bond increment' method.
<ul>
<li><b>'Si'</b> : 2.05</li>
<li><b>'Al'</b> : 1.75</li>
<li><b>'O'</b> bonded to two silicons: -1.025</li>
<li><b>'O'</b> bonded to one silicon and one aluminum: -1.20</li>
<li><b>'Na'</b> : 1.0</li>
<li><b>'C'</b> : all alkane carbons have a 0.0 charge.</li>
</ul>
</ul>
<a href="../towhee_capabilities.html">Return to the Towhee Capabilities web page</a>
<p> </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 -->September 07, 2005<!-- #EndDate -->
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