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@ -363,7 +363,7 @@ commands like <a class="reference internal" href="pair_coeff.html"><span class="
<a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a>. See <a class="reference internal" href="Section_tools.html"><span class="doc">Section_tools</span></a>
for additional tools that can use CHARMM or AMBER to assign force
field coefficients and convert their output into LAMMPS input.</p>
<p>See <a class="reference internal" href="special_bonds.html#mackerell"><span class="std std-ref">(MacKerell)</span></a> for a description of the CHARMM force
<p>See <a class="reference internal" href="#howto-mackerell"><span class="std std-ref">(MacKerell)</span></a> for a description of the CHARMM force
field. See <a class="reference internal" href="special_bonds.html#cornell"><span class="std std-ref">(Cornell)</span></a> for a description of the AMBER force
field.</p>
<p>These style choices compute force field formulas that are consistent
@ -587,7 +587,7 @@ computations between frozen atoms by using this command:</p>
<div class="section" id="tip3p-water-model">
<span id="howto-7"></span><h2>6.7. TIP3P water model</h2>
<p>The TIP3P water model as implemented in CHARMM
<a class="reference internal" href="special_bonds.html#mackerell"><span class="std std-ref">(MacKerell)</span></a> specifies a 3-site rigid water molecule with
<a class="reference internal" href="#howto-mackerell"><span class="std std-ref">(MacKerell)</span></a> specifies a 3-site rigid water molecule with
charges and Lennard-Jones parameters assigned to each of the 3 atoms.
In LAMMPS the <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a> command can be used to hold
the two O-H bonds and the H-O-H angle rigid. A bond style of
@ -766,7 +766,7 @@ the partial charge assignemnts change:</p>
<div class="line">H charge = 0.4238</div>
<div class="line"><br /></div>
</div>
<p>See the <a class="reference internal" href="fix_temp_berendsen.html#berendsen"><span class="std std-ref">(Berendsen)</span></a> reference for more details on both
<p>See the <a class="reference internal" href="#howto-berendsen"><span class="std std-ref">(Berendsen)</span></a> reference for more details on both
the SPC and SPC/E models.</p>
<p>Wikipedia also has a nice article on <a class="reference external" href="http://en.wikipedia.org/wiki/Water_model">water models</a>.</p>
<hr class="docutils" />
@ -2731,7 +2731,7 @@ pairs as chunks.</p>
model, representes induced dipoles by a pair of charges (the core atom
and the Drude particle) connected by a harmonic spring. The Drude
model has a number of features aimed at its use in molecular systems
(<a class="reference internal" href="tutorial_drude.html#lamoureux"><span class="std std-ref">Lamoureux and Roux</span></a>):</p>
(<a class="reference internal" href="#howto-lamoureux"><span class="std std-ref">Lamoureux and Roux</span></a>):</p>
<ul class="simple">
<li>Thermostating of the additional degrees of freedom associated with the
induced dipoles at very low temperature, in terms of the reduced
@ -2776,7 +2776,7 @@ using Thole functions through the the <a class="reference internal" href="pair_t
with a Coulomb pair style. It may be useful to use <em>coul/long/cs</em> or
similar from the CORESHELL package if the core and Drude particle come
too close, which can cause numerical issues.</p>
<p id="berendsen"><strong>(Berendsen)</strong> Berendsen, Grigera, Straatsma, J Phys Chem, 91,
<p id="howto-berendsen"><strong>(Berendsen)</strong> Berendsen, Grigera, Straatsma, J Phys Chem, 91,
6269-6271 (1987).</p>
<p id="cornell"><strong>(Cornell)</strong> Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).</p>
@ -2784,7 +2784,7 @@ Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).</p>
J Chem Phys, 120, 9665 (2004).</p>
<p id="ikeshoji"><strong>(Ikeshoji)</strong> Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261
(1994).</p>
<p id="mackerell"><strong>(MacKerell)</strong> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
<p id="howto-mackerell"><strong>(MacKerell)</strong> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).</p>
<p id="mayo"><strong>(Mayo)</strong> Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).</p>
@ -2794,7 +2794,7 @@ Phys, 79, 926 (1983).</p>
<p id="shinoda"><strong>(Shinoda)</strong> Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).</p>
<p id="mitchellfinchham"><strong>(Mitchell and Finchham)</strong> Mitchell, Finchham, J Phys Condensed Matter,
5, 1031-1038 (1993).</p>
<p id="lamoureux"><strong>(Lamoureux and Roux)</strong> G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)</p>
<p id="howto-lamoureux"><strong>(Lamoureux and Roux)</strong> G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)</p>
</div>
</div>