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<title>MCCCS Towhee (Alavi et al 2005)</title>
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<div align="center"> <font size="5"> <b><font face="Arial, Helvetica, sans-serif"><a name="top"></a>MCCCS
Towhee (Alavi <i>et al.</i> 2005)</font></b> </font> </div>
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<td width="697" valign="top"> <b>Overview</b>
<ul>
This section covers the Alavi <i>et al.</i> 2005 (Alavi2005) force field as it is implemented into
the towhee_ff_Alavi2005 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.
Note that this a Lennard-Jones (12-6) force field and can only be combined with
other Lennard-Jones (12-6) 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.
</ul>
<b>References for Alavi2005</b>
<ul>
This force field was published in a single paper where it was used along with the
<a href="spce.html">SPC/E</a> force field for water.
<ul>
<li><a href="../references.html#alavi_et_al_2005">Alavi <i>et al.</i> 2005</a></li>
</ul>
</ul>
<b>Alavi <i>et al.</i> 2005 in Towhee</b>
<ul>
The official force field name for Alavi <i>et al.</i> 2005 in Towhee is 'Alavi2005'. 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. This force field was designed to work with the
<a href="spce.html">SPC/E</a> water model. This force field uses a three site model for H<sub>2</sub>
as described below.
Please note that the capitalization and spacing pattern is important
and must be followed exactly as listed here.
<ul>
<li><b>'H2-com'</b> : the center of mass of an H<sub>2</sub> molecule. This atom type has no mass itself
and should be bonded to 2 <b>H2-end</b> sites.
</li>
<li><b>'H2-end'</b> : hydrogen atom in H<sub>2</sub>. This atom type represents the mass point for
each hydrogen atom and should be bonded to the <b>H2-com</b> site.
</li>
</ul>
</ul>
<b>Coulombic interactions</b>
<ul>
Alavi2005 assigns a point charge to the H<sub>2</sub> mass sites and also to the center of mass location.
The bond increment method is implemented for this forcefield and can be used to automatically assign
appropriate charges.
Please see the <a href="../inpstyle/inpstyle_2.html">inpstyle 2</a> documentation for
further information on enabling this option.
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">H2-end</font> - <font color="green">H2-com</font>: 0.4932</li>
</ul>
</ul>
<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 26, 2005<!-- #EndDate -->
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