<html>
<head>
<title>MCCCS Towhee (Catlow/Faux)</title>
</head>
<body bgcolor="#FFFFFF" text="#000000">
<table width="675" border="0" cellspacing="0" cellpadding="0" height="590">
<tr>
<td colspan="2" height="29">
<div align="center"> <font size="5"> <b><font face="Arial, Helvetica, sans-serif"><a name="top"></a>MCCCS
Towhee (Catlow/Faux)</font></b> </font> </div>
</td>
</tr>
<A href="http://sourceforge.net">
<IMG src="http://sourceforge.net/sflogo.php?group_id=87039&type=5" width="210" height="62" border="0"
alt="SourceForge.net Logo" align="right"/>
</A>
<tr>
<td width="18" height="371" valign="top">
<p> </p>
<p> </p>
</td>
<td width="697" valign="top"> <b>Overview</b>
<ul>
This section covers the Catlow and Faux force field as it is implemented into
the towhee_ff_CatlowFaux file in the ForceFields directory. All of the Towhee atom types for the Catlow and Faux force
field are listed, along with a short description of their meanings.
Note that the Catlow and Faux force fields are a hybrid of Lennard-Jones (12-6)
and an exponential replusion and cannot be combined with any other force fields.
I would like to acknowledge David A. Faux for providing
very useful guidance about implementing Catlow and Faux force field.
Any discrepencies (especially typos)
from the published force field 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 Catlow and Faux</b>
<ul>
This force field comes from a variety of sources. Several authors have used zeolite parameters that are
similar (but often slightly different) to those published in
<ul>
<li><a href="../references.html#jackson_catlow_1988">Jackson and Catlow 1988</a></li>
</ul>
The implementation in Towhee uses the zeolite (OZ, Al, Si, Na) parameters as modified in
<ul>
<li><a href="../references.html#faux_et_al_1997">Faux <i>et al.</i> 1997</a></li>
</ul>
with the exception that there is a typo in Table 1 of that paper which listed harmonic terms for the Al-OZ-Si and
Si-OZ-Al angles. That should instead be harmonic parameters for the OZ-Al-OZ and OZ-Si-OZ angles. Note that these
harmonic terms are in addition to the normal van der Waals and coulombic interaction between these atoms. There is
no additional harmonic term for either the Al-OZ-Si or Si-OZ-Al (personal communication between M.G. Martin and D.A. Faux
February 13, 2001).
<dt>The hydrocarbon (Cc and Hc) nonbonded parameters, and the cross terms with OZ, Al, Si (note the cross terms are set to zero
for Cc-Si, Cc-Al, Hc-Si, and Hc-Al) are from
<ul>
<li><a href="../references.html#raj_et_al_1999">Raj <i>et al.</i> 1999</a>
</ul>
However, we wanted a fully flexible alkane model so we used the bonded parameters from
<ul>
<li><a href="../references.html#catlow_et_al_1991">Catlow <i>et al.</i> 1991</a></li>
</ul>
instead of the semi-rigid model from <a href="../references.html#raj_et_al_1999">Raj <i>et al.</i> 1999</a>.
<dt>I also concocted some cross terms for Na-Cc and Na-Hc by combining
<a href="../references.html#raj_et_al_1999">Raj <i>et al.</i> 1999</a> with sodium parameters from
<ul>
<li><a href="../references.html#aqvist_1990">Aqvist 1990</a></li>
</ul>
using geometric mixing rules.
</ul>
<b>Catlow/Faux in Towhee</b>
<ul>
The official force field name for these parameters is 'CatlowFaux' (starting with version 3.2.9) Here I list all of the Catlow and Faux
atom names for use in the towhee_input file, along with a brief description of what atoms we are talking about.
Please note that the capitalization and spacing pattern is important
and must be followed exactly as listed here.
<ul>
<li><b>'Cc'</b> : carbon in an alkane</li>
<li><b>'Hc'</b> : hydrogen bonded to carbon in an alkane</li>
<li><b>'Al'</b> : aluminum in a zeolite</li>
<li><b>'Na'</b> : sodium ion</li>
<li><b>'OZ'</b> : oxygen in a zeolite</li>
<li><b>'Si'</b> : silicon in a zeolite</li>
</ul>
</ul>
<b>Coulombic Interactions</b>
<ul>
This force field uses point charges on atomic centers. Here we list suggested charges for each of the
atom types in this force field.
<dt>Catlow charges are only listed for n-octane in <a href="../references.html#raj_et_al_1999">Raj <i>et al.</i> 1999</a>.
It is not obvious how to interpolate those charges for other alkanes, but it would be consistent with the reasoning in that paper
to set all of the Hydrogens to 0.100 and then evenly divide the counter charge across all of the carbons.
<ul>
<li><b>'Cc'</b> : In n-octane this is set to -0.225. One possible way to do this for general alkanes would be
a charge equal to the number of hydrogens times the charge on each hydrogen divided by the total number of carbons.</li>
<li><b>'Hc'</b> : In n-octane this is set to 0.100. One possible way to do this for general alkanes would be to
always set the Hc charge to 0.100 and adjust the counter charge on the carbons.</li>
</ul>
<dt>Faux charges from <a href="../references.html#faux_et_al_1997">Faux <i>et al.</i> 1997</a></dt>
<ul>
<li><b>'Al'</b> : 2.775</li>
<li><b>'Na'</b> : 1.0</li>
<li><b>'OZ'</b> : -1.86875</li>
<li><b>'Si'</b> : 3.7</li>
</ul>
</ul>
<b>Improper torsions</b>
<ul>
There are no improper torsions in the Catlow or Faux force fields.
</ul>
<b>Proteins</b>
<ul>
The Catlow and Faux force fields are designed for zeolites and are not suited for proteins.
</ul>
<a href="../towhee_capabilities.html">Return to the Towhee Capabilities web page</a>
<p> </p>
</td>
</tr>
</table>
<hr width="715" align="left">
<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 -->
</font> <br>
</body>
</html>
distrib
>
Fedora
>
14
>
x86_64
>
media
>
updates
>
by-pkgid
>
2f8321c8e2a11ea8b160a642cfc9fd7f
>
files
>
164
