<html>
<head>
<title>MCCCS Towhee (Shah2004)</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 (Shah and Maginn 2004)</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 Shah and Maginn 2004 (Shah2004) force field as it is implemented into
the towhee_ff_Shah2004 file in the ForceFields directory. This force field was
designed for an ionic liquid of 1-<i>n</i>-butyl-3-methylimidazolium [bmim] hexafluorophosphate [PF<sub>6</sub>].
Note that this is a Lennard-Jones force field that uses the 'Lorentz-Berthelot' mixing rules.
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 Shah and Maginn 2004</b>
<ul>
This forcefield is described in a single paper.
<ul>
<li><a href="../references.html#shah_maginn_2004">Shah and Maginn 2004</a></li>
</ul>
</ul>
<b>Typos and comments for Shah and Maginn 2004</b>
<ul>
<li>Full Lennard-Jones interactions are used for 1-4 interactions, while the Coulombic 1-4 terms are scaled by 1/2
[personal communication between E.J. Maginn and M.G. Martin 04-21-2006]. This is with the execption of the ring
dihedrals that are held rigid and so there is no reason to compute the 1-4 terms.
</li>
<li>Note that the coordinates presented for the PF<sub>6</sub> structure result in asymmetric bond lengths and bending
angles. I have inlcluded that as an atom-specific implementation of PF<sub>6</sub>, and I have also included an
option for symmetric PF<sub>6</sub> using the bond length from
<a href="../references.html#morrow_maginn_2002">Morrow and Maginn 2002</a>.
</li>
<li>Note that all of the rigid interactions in this molecule means you need to start the simulation using a template for
both molecules. Coordinates suitable for a template are found in Table 1 of
<a href="../references.html#shah_maginn_2004">Shah and Maginn 2004</a>.
</li>
</ul>
<b>Shah and Maginn 2004 in Towhee</b>
<ul>
The official force field name for Shah and Maginn 2004 in Towhee is 'Shah2004'. Here is the list
of atom names for use in the towhee_input file, along with a brief description. These names correspond to those
used in <a href="../references.html#shah_maginn_2004">Shah and Maginn 2004</a>. I have also included an option
for a symmetric PF<sub>6</sub> using a perfect octahedral geometry and a P-F bond length taken from
<a href="../references.html#morrow_maginn_2002">Morrow and Maginn 2002</a>.
Please note that the capitalization and spacing pattern is important
and must be followed exactly as listed here.
<ul>
<li><b>'N1'</b> : Ring Nitrogen bonded to C2, C5, and C7 in bmim</li>
<li><b>'C2'</b> : Ring Carbon (and an implicit bonded hydrogen) bonded to N1 and N3 in bmim</li>
<li><b>'N3'</b> : Ring Nitrogen bonded to C2, C4, and C6 in bmim</li>
<li><b>'C4'</b> : Ring Carbon (and an implicit bonded hydrogen) bonded to N3 and C5 in bmim</li>
<li><b>'C5'</b> : Ring Carbon (and an implicit bonded hydrogen) bonded to N1 and C4 in bmim</li>
<li><b>'C6'</b> : methyl Carbon (and three implicit bonded hydrogens) bonded to N3 in bmim</li>
<li><b>'C7'</b> : methylene Carbon (and two implicit bonded hydrogens) bonded to N1 and C8 in bmim</li>
<li><b>'C8'</b> : methylene Carbon (and two implicit bonded hydrogens) bonded to C7 and C9 in bmim</li>
<li><b>'C9'</b> : methylene Carbon (and two implicit bonded hydrogens) bonded to C8 and C10 in bmim</li>
<li><b>'C10'</b> : methyl Carbon (and three implicit bonded hydrogens) bonded to C9 in bmim</li>
<li><b>'P'</b> : P in hexafluorophosphate</li>
<li><b>'F'</b> : generic F in hexafluorophosphate if you want to use the symmetric bond length and
bending angle version of that molecule.
</li>
<li><b>'F1'</b> : specific F in hexafluorophosphate if you want to use the assymmetric bond length and
bending angle version of that molecule.
</li>
<li><b>'F2'</b> : specific F in hexafluorophosphate if you want to use the assymmetric bond length and
bending angle version of that molecule.
</li>
<li><b>'F3'</b> : specific F in hexafluorophosphate if you want to use the assymmetric bond length and
bending angle version of that molecule.
</li>
<li><b>'F4'</b> : specific F in hexafluorophosphate if you want to use the assymmetric bond length and
bending angle version of that molecule.
</li>
<li><b>'F5'</b> : specific F in hexafluorophosphate if you want to use the assymmetric bond length and
bending angle version of that molecule.
</li>
<li><b>'F6'</b> : specific F in hexafluorophosphate if you want to use the assymmetric bond length and
bending angle version of that molecule.
</li>
</ul>
</ul>
<b>Coulombic interactions</b>
<ul>
This force field uses point charges and has been set up to assign the point charges using the bond increment method.
The charges for bmim are assigned according to Table 2 of
<a href="../references.html#shah_maginn_2004">Shah and Maginn 2004</a>.
</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 -->April 27, 2006<!-- #EndDate -->
</font> <br>
</body>
</html>
distrib
>
Fedora
>
14
>
x86_64
>
media
>
updates
>
by-pkgid
>
2f8321c8e2a11ea8b160a642cfc9fd7f
>
files
>
209
