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<div align="center"> <font size="5"> <b><font face="Arial, Helvetica, sans-serif"><a name="top"></a>MCCCS
Towhee (NERD Version 3)</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 NERD Version 3 United Atom (NERDv3) force field as it is implemented into
the towhee_ff_NERDv3 file in the ForceFields directory. The NERD force field has had several minor
changes to parameters as time as progresses so I have broken each of these changes into a different
version of the force field. All of the Towhee atom types for this force
field are listed, along with a short description of their meanings.
Note that NERDv3 is a Lennard-Jones (12-6) force field and can only be combined with
other Lennard-Jones (12-6) force fields. I would like to thank Nicholas du Preez for initiating
the implementation of this force field into Towhee.
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 NERD Version 3</b>
<ul>
What I term NERD Version 3 is described in a single paper (listed here) plus all of the
original <a href="nerdv1.html">NERDv1</a> and <a href="nerdv2.html">NERDv2</a> references.
Note that some of the terms in those original works have been superceded by later publications.
<ul>
<li><a href="../references.html#khare_et_al_2004">Khare <i>et al.</i> 2004</a></li>
</ul>
</ul>
<b>NERDv3 in Towhee</b>
<ul>
The official force field name for NERD Version 2 United Atom in Towhee is 'NERDv3'. 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. NERDv3 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>'CH4'</b> : sp<sup>3</sup> carbon plus the 4 hydrogens bonded to it (united-atom) in methane.</li>
<li><b>'CH3sp3eth'</b> : sp<sup>3</sup> carbon plus the 3 hydrogens bonded to it (united-atom) in ethane.</li>
<li><b>'CH3sp3pro'</b> : sp<sup>3</sup> carbon plus the 3 hydrogens bonded to it (united-atom) in propane.</li>
<li><b>'CH3sp3isob'</b> : sp<sup>3</sup> carbon plus the 3 hydrogens bonded to it (united-atom) in isobutane
(2-methylpropane).</li>
<li><b>'CH3sp32mb'</b> : sp<sup>3</sup> carbon plus the 3 hydrogens bonded to it (united-atom) bonded to
a CH group in 2-methylbutane.</li>
<li><b>'CH3sp3neop'</b> : sp<sup>3</sup> carbon plus the 3 hydrogens bonded to it (united-atom) bonded to
a C group in neopentane (2,2-dimethyl propane).</li>
<li><b>'CH3sp322db'</b> : sp<sup>3</sup> carbon plus the 3 hydrogens bonded to it (united-atom) bonded to
a C group in 2,2-dimethylbutane.</li>
<li><b>'CH3sp3pene'</b> : sp<sup>3</sup> carbon plus the 3 hydrogens bonded to it (united-atom) bonded to
an sp<sup>2</sup> CH group in propene.</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>'CH2sp3'</b> : sp<sup>3</sup> carbon plus the 2 hydrogens bonded to it (united-atom).</li>
<li><b>'CHsp3'</b> : sp<sup>3</sup> carbon plus the 1 hydrogen bonded to it (united-atom).</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>'CH2sp2eth'</b> : sp<sup>2</sup> carbon plus the 2 hydrogens bonded to it (united-atom) in ethene.</li>
<li><b>'CH2sp2prim'</b> : sp<sup>2</sup> carbon plus the 2 hydrogens bonded to it (united-atom) in a primary alkene.</li>
<li><b>'CHsp2'</b> : sp<sup>2</sup> carbon plus the 1 hydrogen bonded to it (united-atom) in a primary alkene.</li>
<dt><font color="red">Hydrogen</font></dt>
<li><b>'H_o'</b> : hydrogen bonded to oxygen.</li>
<li><b>'H_s'</b> : hydrogen bonded to sulfur.</li>
<dt><font color="red">Oxygen</font></dt>
<li><b>'Osp3'</b> : sp<sup>3</sup> hybridized oxygen single bonded to two atoms.</li>
<dt><font color="red">Sulfur</font></dt>
<li><b>'S_sh2'</b> : sulfur in dihydrogen sulfide.</li>
</ul>
</ul>
<b>Coulombic interactions</b>
<ul>
Most atoms do not have a charge when using the NERDv3 forcefield. Exceptions are listed below.
<dt><font color="red">SH<sup>2</sup></font> (from <a href="../references.html#nath_2003">Nath 2003</a>)</dt>
<li><b>'H_s'</b> : 0.124</li>
<li><b>'S_sh2'</b> : -0.248</li>
<dt><font color="red">alcohols</font> (from <a href="../references.html#khare_et_al_2004">Khare <i>et al.</i> 2004</a>)</dt>
<li><b>'H_o'</b> : 0.420</li>
<li><b>'Osp3'</b> : -0.710</li>
<li><b>'CH2sp3'</b> (bonded to the oxygen): 0.290</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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