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<title>MCCCS Towhee (TraPPE United Atom Flexible Bonds)</title>
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<div align="center"> <font size="5"> <b><font face="Arial, Helvetica, sans-serif"><a name="top"></a>MCCCS
Towhee (TraPPE United Atom Flexible Bonds)</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 TraPPE United Atom Flexible Bonds (TraPPE-UAf) force field as it is implemented into
the towhee_ff_TraPPE-UAf 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. For
more information about the TraPPE force fields see the
<a href="http://siepmann6.chem.umn.edu/">Siepmann group web site</a>.
Note that TraPPE United Atom Flexible bonds is a Lennard-Jones (12-6) force field and can only be combined with
other Lennard-Jones (12-6) force fields. This forcefield is a subset of the rigid bond
<a href="trappeua.html">TraPPE-UA</a> force field with the change that the bond lengths are no longer rigid and
are instead flexible using parameters from some other papers.
Any discrepencies (especially typos)
from the published TraPPE-UA force field values had better not exist considering I helped create this
force field.
If someone does find a discrepancy with the published values I would be extremely grateful
if they let me know about it. I welcome feedback on how this implementation compares with other programs.
</ul>
<b>References for TraPPE-UAf</b>
<ul>
TraPPE-UAf is still under development by the Siepmann group. The alkane parameters are taken from the first
two TraPPE papers, and the flexible bond lengths are from Mundy <i>et al.</i>.
<ul>
<li><a href="../references.html#mundy_et_al_1996">Mundy <i>et al.</i> 1996</a></li>
<li><a href="../references.html#martin_siepmann_1998_jpcb">Martin and Siepmann 1998 (JPCB)</a></li>
<li><a href="../references.html#martin_siepmann_1998_tca">Martin and Siepmann 1998 (TCA)</a></li>
</ul>
</ul>
<b>Typos and comments for TraPPE-UAf</b>
<ul>
Please see the closely related <a href="trappeua.html">TraPPE-UA</a> force field for typos and comments about
this force field.
</ul>
<b>TraPPE-UAf in Towhee</b>
<ul>
The official force field name for TraPPE United Atom Flexible Bonds in Towhee is 'TraPPE-UAf'. Here I list all of
the TraPPE-UAf atom names for use in the towhee_input file, along with a brief description. These atom name are
the same as those in the rigid bond <a href="trappeua.html">TraPPE-UA</a> force field and have the same meanings.
Please note that the capitalization and spacing pattern is important
and must be followed exactly as listed here.
<ul>
<dt><font color="red">Carbon (not bonded to any hydrogens)</font></dt>
<li><b>'Ccccc(sp3)'</b> : an sp<sup>3</sup> carbon.
This atom is single bonded to four carbon atoms.
Bond name <font color="green">Csp3</font>.
</li>
<dt><font color="red">Carbon (united atom including 1 bonded hydrogen)</font></dt>
<li><b>'CHccc(sp3)'</b> : united-atom consisting of an sp<sup>3</sup> carbon and one bonded hydrogen.
This united-atom is single bonded to three carbon atoms.
Bond name <font color="green">Csp3</font>.
</li>
<dt><font color="red">Carbon (united atom including 2 bonded hydrogens)</font></dt>
<li><b>'CH2**(sp3)'</b> : united-atom consisting of an sp<sup>3</sup> carbon and two bonded hydrogens.
This united-atom is single bonded to any two non-hydrogen atoms.
Bond name <font color="green">Csp3</font>.
</li>
<dt><font color="red">Carbon (united atom including 3 bonded hydrogens)</font></dt>
<li><b>'CH3*(sp3)'</b> : united-atom consisting of an sp<sup>3</sup> carbon and three bonded hydrogens.
This united-atom is single bonded to any non-hydrogen atom.
Bond name <font color="green">Csp3</font>.
</li>
<dt><font color="red">Carbon (united atom including 4 bonded hydrogens)</font></dt>
<li><b>'CH4'</b> : methane</li>
</ul>
</ul>
<b>Coulombic interactions</b>
<ul>
TraPPE-UA uses atom-centered point charges to represent the electrostatic interactions. There are no coulombic
interactions for the atom types currently implemented in this force field.
Here I list the bond increments using the bond names listed above. The value of the bond increment is added
to the first atom listed and subtracted from the second atom listed.
<ul>
<li><font color="green">Csp3</font> - <font color="green">Csp3</font>: 0.0</li>
</ul>
</ul>
<b>Improper torsions</b>
<ul>
TraPPE-UAf does not utilize improper torsions.
</ul>
<a href="../towhee_capabilities.html">Return to the Towhee Capabilities web page</a>
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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 -->November 12, 2005<!-- #EndDate -->
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