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<title>MCCCS Towhee (COMPASSv1)</title>
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<div align="center"> <font size="5"> <b><font face="Arial, Helvetica, sans-serif"><a name="top"></a>MCCCS
Towhee (COMPASSv1)</font></b> </font> </div>
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<td width="697" valign="top"> <b>Overview</b>
<ul>
This section covers the COMPASSv1 force field as it is implemented into
the towhee_ff_COMPASSv1 file in the ForceFields directory. All of the Towhee atom types for the COMPASSv1 force field
are listed, along with a short description of their meanings. For more
information about the COMPASSv1 force field see the <a href="http://www.accelrys.com">Accelrys
web site</a>. The COMPASSv1 force field is maintained by researchers at
Accelrys and only a portion of it has been published in the peer-reviewed
literature. I have only incorporated those parts that have been published.
Note that COMPASSv1 is a Lennard-Jones (9-6) force field and can only be
combined with other Lennard-Jones (9-6) force fields. I would like to
acknowledge David Rigby for providing very useful guidance about implementing
COMPASSv1. Any discrepencies (especially typos) from the published COMPASSv1
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 COMPASSv1</b>
<ul>
The COMPASS family of forcefield is an ongoing subject of further parameterization.
The authors of the forcefield periodically revisit old parameters and refit them to
additional data. Towhee defines COMPASSv1 as the parameters published in the following
series of papers.
<ul>
<li><a href="../references.html#rigby_et_al_1997">Rigby <i>et al.</i> 1997</a></li>
<li><a href="../references.html#sun_rigby_1997">Sun and Rigby 1997</a></li>
<li><a href="../references.html#sun_1998">Sun 1998</a></li>
<li><a href="../references.html#sun_et_al_1998">Sun <i>et al.</i> 1998</a></li>
<li><a href="../references.html#bunte_sun_2000">Bunte and Sun 2000</a></li>
<li><a href="../references.html#yang_et_al_2000">Yang <i>et al.</i> 2000</a></li>
<li><a href="../references.html#mcquaid_et_al_2003">McQuaid <i>et al.</i> 2003</a></li>
</ul>
</ul>
<b>Typos and clarifications for COMPASSv1</b>
<ul>
With the large size of the COMPASSv1 force field it is not surprising that
there are a few typos in the published literature. Here I summarize and
clarify differences in my implementation from the literature.
<ul>
<li> There are full van der Waals and coulombic interactions between
atoms connected by three bonds (1-4 interactions).</li>
<li> Rigby <i>et al.</i> 1997: In the angle-angle-torsion term for ha-c4-c4-o2
the ijk/jkl/ijkl constant is set to 20.2006 while it should actually
be -20.2006 [personal communication between M.G. Martin and D. Rigby
August 09, 2001]</li>
<li> Sun 1998: The mixing rules for epsilon are stated incorrectly.
The term in the denominator should read (r<sub>i</sub><sup>0</sup>)<sup>6</sup>
+ (r<sub>j</sub><sup>0</sup>)<sup>6</sup>. The + is missing in that
paper.</li>
<li> Sun 1998: In the End Bond-Torsion for c4-c4-c4-c4 the K-L/I-J-K-L
k1 value is set to 0.0000 and I think it should be set to the same
value as the I-J/I-J-K-L k1 value of -0.0732. This correction was
made in Towhee.</li>
</ul>
</ul>
<b>COMPASSv1 in Towhee</b>
<ul>
The official force field name for COMPASSv1 in Towhee is 'COMPASSv1'. Here
I list all of the COMPASSv1 atom names for use in the towhee_input file,
along with a brief description taken from the COMPASSv1 papers. I have added
some comments where I thought clarification was needed, these are all
in [square brackets]. The COMPASSv1 naming convention has the first letter
as the element, the second character is the number of bonds to that element,
and the third character is a bit of a wildcard. Please note that the capitalization
and spacing pattern is important and must be followed exactly as listed
here.
<ul>
<dt><font color="red">Argon</font></dt>
<li><b>'ar'</b> : argon</li>
<dt><font color="red">Carbon</font></dt>
<li><b>'c1o'</b> : carbon in CO</li>
<li><b>'c2='</b> : carbon in CO<sub>2</sub> and CS<sub>2</sub></li>
<li><b>'c3a'</b> : aromatic carbon [carbon with 3 bonds, aromatic]</li>
<li><b>'c4'</b> : generic sp<sup>3</sup> carbon [carbon with 4 bonds,
use only if none of the other c4 special cases are valid]</li>
<li><b>'c43'</b> : sp<sup>3</sup> carbon with three heavy atoms attached</li>
<li><b>'c44'</b> : sp<sup>3</sup> carbon with four heavy atoms attached</li>
<li><b>'c4o'</b> : alpha carbon [sp<sup>3</sup> carbon bonded to an
oxygen in an alcohol or ether]</li>
<li><b>'c4z'</b> : carbon, sp<sup>3</sup>, bonded to -N<sub>3</sub></li>
<dt><font color="red">Helium</font></dt>
<li><b>'he'</b> : helium</li>
<dt><font color="red">Hydrogen</font></dt>
<li><b>'h1'</b> : nonpolar hydrogen [hydrogen bonded to carbon]</li>
<li><b>'h1h'</b> : hydrogen in H<sub>2</sub></li>
<li><b>'h1o'</b> : strongly polar hydrogen [hydrogen bonded to oxygen]</li>
<dt><font color="red">Krypton</font></dt>
<li><b>'kr'</b> : krypton</li>
<dt><font color="red">Neon</font></dt>
<li><b>'ne'</b> : neon</li>
<dt><font color="red">Nitrogen</font></dt>
<li><b>'n1n'</b> : nitrogen in N<sub>2</sub></li>
<li><b>'n1o'</b> : nitrogen in NO</li>
<li><b>'n1z'</b> : nitrogen, terminal atom in -N<sub>3</sub></li>
<li><b>'n2='</b> : nitrogen [nitrogen with a single bond and a double
bond]</li>
<li><b>'n2o'</b> : nitrogen in NO<sub>2</sub></li>
<li><b>'n2z'</b> : nitrogen, first atom in -N<sub>3</sub></li>
<li><b>'n2t'</b> : nitrogen, central atom in -N<sub>3</sub></li>
<li><b>'n3o'</b> : nitrogen in nitro group</li>
<dt><font color="red">Oxygen</font></dt>
<li><b>'o1='</b> : oxygen in NO<sub>2</sub> and SO<sub>2</sub></li>
<li><b>'o1=*'</b> : oxygen in CO<sub>2</sub></li>
<li><b>'o12'</b> : oxygen in nitro group (-NO<sub>2</sub>)</li>
<li><b>'o1c'</b> : oxygen in CO</li>
<li><b>'o1n'</b> : oxygen in NO</li>
<li><b>'o1o'</b> : oxygen in O<sub>2</sub></li>
<li><b>'o2'</b> : generic oxygen with two bonds</li>
<li><b>'o2e'</b> : ether oxygen</li>
<li><b>'o2h'</b> : hydroxyl oxygen [alcohol oxygen]</li>
<li><b>'o2n'</b> : oxygen in nitrates</li>
<dt><font color="red">Phosphorous</font></dt>
<li><b>'p4='</b> : phosphorous [phosphorous with three single bonds
and a double bond]</li>
<dt><font color="red">Silicon</font></dt>
<li><b>'si4'</b> : generic silicon with four bonds attached</li>
<li><b>'si4c'</b> : a subset of Si4, non-hydrogen atom attached</li>
<dt><font color="red">Sulfur</font></dt>
<li><b>'s1='</b> : sulfur in CS<sub>2</sub></li>
<li><b>'s2='</b> : sulfur in SO<sub>2</sub></li>
<li><b>'xe'</b> : xenon</li>
</ul>
</ul>
<b>Coulombic Interactions</b>
<ul>
COMPASSv1 uses point charges to represent the electrostatic interactions on molecules.
They have devised an automated system for assigning the point charges on each atom that
depends on the atom types, and the types of atoms bonded to each atom. This system is
implemented into Towhee Version 4.4.0 and later. In order to anable automatic charge assignment
you use <b>inpstyle</b> 2 in combination with <b>charge_assignment</b> 'bond increment'.
Please see the <a href="../inpstyle/inpstyle_2.html">inpstyle 2</a> documentation for
further information on enabling this option.
</ul>
<b>Angle-Angle cross terms</b>
<ul>
COMPASSv1 is a class 2 force field and so you do need to include angle-angle
cross terms. However, I have automated the detection and type determination
for COMPASSv1 so I would recomend using the inpstyle = 2 feature in order
to determine these. The rest of the fancy cross terms for COMPASSv1 are
included in the bending angle and dihedral angle potentials.
</ul>
<b>Improper torsions</b>
<ul>
Improper torsions are not automatically generated by the Towhee code as
the rules for determining where they are applied are not always straight-forward.
COMPASSv1 exclusively uses the out-of-plane version of the improper torsions,
and they are typically centered on an sp<sup>2</sup> atom in order to
enforce planarity with its three neighbors. These torsions are listed
in the COMPASSv1 literature as i-j-k-l where the angle is the dihedral between
j-i-k and i-k-l, and the bonding pattern is i, k, and l all bonded to
atom j, and also not bonded to each other. In the towhee_input file this
out-of-plane improper torsion is listed only for atom j, and the atom
order there is i, k, l. Unfortunately, I have not yet set up the automation
for determining the improper types for COMPASSv1 yet as the impropers are
almost exclusively used on aromatics, and I have not yet tested the code
for those molecules. You will need to look in fftorsion.F in order to
find the types if you need the improper torsions for COMPASSv1.
</ul>
<a href="../towhee_capabilities.html">Return to the Towhee Capabilities web page</a>
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<a href="http://www.sandia.gov/dis.htm"><font size="2"></font></a> </font> <br>
<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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