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<div align="center"> <font size="5"> <b><font face="Arial, Helvetica, sans-serif"><a name="top"></a>MCCCS
Towhee (Sum <i>et al.</i> 2003)</font></b> </font> </div>
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<p> </p>
<p> </p>
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<td width="697" valign="top"> <b>Overview</b>
<ul>
This section covers the Sum <i>et al.</i> 2003 United Atom (Sum2003) force field as it is implemented into
the towhee_ff_Sum2003 file in the ForceFields directory. This forcefield is an extension to the
<a href="nerdv2.html">NERDv2</a> force field that allows the simulation of acetates and glycerols.
I would like to acknowledge Mary Biddy for providing useful guidence about implementing this force field.
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 Sum <i>et al.</i> 2003</b>
<ul>
See the <a href="nerdv2.html">NERD Version 2</a> force field documentation for the references for the
alkane chains. The extensions to that force field are published in a single paper.
<ul>
<li><a href="../references.html#sum_et_al_2003">Sum <i>et al.</i> 2003</a></li>
</ul>
</ul>
<b>Sum2003 in Towhee</b>
<ul>
The official force field name for Sum <i>et al.</i> United Atom in Towhee is 'Sum2003'. 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. Sum2003 is a united-atom force field which lumps
hydrogens onto their neighboring carbons. Note that hydrogens that are bonded to atoms other than carbon
are not lumped onto their neighboring atoms. 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>'CH3sp3oac'</b> : sp<sup>3</sup> carbon plus the 3 hydrogens bonded to it (united-atom) bonded to
an sp<sup>3</sup> oxygen in an acetate group.</li>
<li><b>'CH3sp3cac'</b> : sp<sup>3</sup> carbon plus the 3 hydrogens bonded to it (united-atom) bonded to
an sp<sup>2</sup> carbon in an acetate group.</li>
<li><b>'CH3sp3mesc'</b> : sp<sup>3</sup> carbon plus the 3 hydrogens bonded to it (united-atom) bonded to
a CH group (methyl side-chain) and not a special case listed above.</li>
<li><b>'CH3sp3etsc'</b> : sp<sup>3</sup> carbon plus the 3 hydrogens bonded to it (united-atom) bonded to
a CH<sub>2</sub> group that is itself bonded to a CH group (ethyl side-chain).</li>
<li><b>'CH3sp3gen'</b> : sp<sup>3</sup> carbon plus the 3 hydrogens bonded to it (united-atom) and not one
of the cases listed above.</li>
<li><b>'CH2sp3oac'</b> : sp<sup>3</sup> carbon plus the 2 hydrogens bonded to it (united-atom) that is bonded
to an sp<sup>3</sup> oxygen in a glycerol.</li>
<li><b>'CH2sp3cac'</b> : sp<sup>3</sup> carbon plus the 2 hydrogens bonded to it (united-atom) that is bonded
to an sp<sup>2</sup> carbon in an acetate group.</li>
<li><b>'CH2sp3'</b> : sp<sup>3</sup> carbon plus the 2 hydrogens bonded to it (united-atom) and not a special case.</li>
<li><b>'CHsp3oac'</b> : sp<sup>3</sup> carbon plus the 1 hydrogen bonded to it (united-atom) that is bonded
to an sp<sup>3</sup> oxygen in a glycerol.</li>
<li><b>'CHsp3'</b> : sp<sup>3</sup> carbon plus the 1 hydrogen bonded to it (united-atom) and not a special case.</li>
<li><b>'Csp3'</b> : sp<sup>3</sup> carbon that is not bonded to any hydrogens.</li>
<dt><font color="red">sp<sup>2</sup> hybridized Carbons</font></dt>
<li><b>'Csp2ac'</b> : sp<sup>2</sup> carbon double bonded to an sp<sup>2</sup> oxygen, single bonded to
an sp<sup>3</sup> oxygen, and single bonded to another carbon in an acetate group.</li>
<dt><font color="red"> Oxygen</font></dt>
<li><b>'Osp3'</b> : sp<sup>3</sup> oxygen bonded to two atoms.</li>
<li><b>'Osp2'</b> : sp<sup>2</sup> oxygen double bonded to a single atom.</li>
</ul>
</ul>
<b>Coulombic interactions</b>
<ul>
Here is the list of charge assignments for methylacetate. It appears that these are also the charges used
for an acetate headgroup on other molecules (e.g. glycerols).
<li><b>'CH3sp3oac'</b> : 0.200</li>
<li><b>'Osp3'</b> : -0.400</li>
<li><b>'Csp2ac'</b> : 0.650</li>
<li><b>'Osp2'</b> : -0.500</li>
<li><b>'CH3sp3cac'</b> : 0.050</li>
</ul>
<b>Improper torsions</b>
<ul>
This force field does not utilize improper torsions.
</ul>
<b>Proteins</b>
<ul>
This force field does not have all of the groups needed for protein simulations.
</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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