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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14498 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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2016-01-26 15:07:02 +00:00
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5
doc/angle_charmm.html
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@ -127,6 +127,9 @@
<div class="section" id="angle-style-charmm-command"> <div class="section" id="angle-style-charmm-command">
<span id="index-0"></span><h1>angle_style charmm command<a class="headerlink" href="#angle-style-charmm-command" title="Permalink to this headline"></a></h1> <span id="index-0"></span><h1>angle_style charmm command<a class="headerlink" href="#angle-style-charmm-command" title="Permalink to this headline"></a></h1>
</div> </div>
<div class="section" id="angle-style-charmm-intel-command">
<h1>angle_style charmm/intel command<a class="headerlink" href="#angle-style-charmm-intel-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="angle-style-charmm-kk-command"> <div class="section" id="angle-style-charmm-kk-command">
<h1>angle_style charmm/kk command<a class="headerlink" href="#angle-style-charmm-kk-command" title="Permalink to this headline"></a></h1> <h1>angle_style charmm/kk command<a class="headerlink" href="#angle-style-charmm-kk-command" title="Permalink to this headline"></a></h1>
</div> </div>
@ -152,7 +155,7 @@ angle_coeff 1 300.0 107.0 50.0 3.0
<p>with an additional Urey_Bradley term based on the distance <em>r</em> between <p>with an additional Urey_Bradley term based on the distance <em>r</em> between
the 1st and 3rd atoms in the angle. K, theta0, Kub, and Rub are the 1st and 3rd atoms in the angle. K, theta0, Kub, and Rub are
coefficients defined for each angle type.</p> coefficients defined for each angle type.</p>
<p>See <a class="reference internal" href="special_bonds.html#mackerell"><span>(MacKerell)</span></a> for a description of the CHARMM force <p>See <a class="reference internal" href="dihedral_charmm.html#mackerell"><span>(MacKerell)</span></a> for a description of the CHARMM force
field.</p> field.</p>
<p>The following coefficients must be defined for each angle type via the <p>The following coefficients must be defined for each angle type via the
<a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a> command as in the example above, or in <a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a> command as in the example above, or in

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doc/angle_charmm.txt
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@ -7,6 +7,7 @@
:line :line
angle_style charmm command :h3 angle_style charmm command :h3
angle_style charmm/intel command :h3
angle_style charmm/kk command :h3 angle_style charmm/kk command :h3
angle_style charmm/omp command :h3 angle_style charmm/omp command :h3

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doc/bond_harmonic.html
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@ -127,6 +127,9 @@
<div class="section" id="bond-style-harmonic-command"> <div class="section" id="bond-style-harmonic-command">
<span id="index-0"></span><h1>bond_style harmonic command<a class="headerlink" href="#bond-style-harmonic-command" title="Permalink to this headline"></a></h1> <span id="index-0"></span><h1>bond_style harmonic command<a class="headerlink" href="#bond-style-harmonic-command" title="Permalink to this headline"></a></h1>
</div> </div>
<div class="section" id="bond-style-harmonic-intel-command">
<h1>bond_style harmonic/intel command<a class="headerlink" href="#bond-style-harmonic-intel-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="bond-style-harmonic-kk-command"> <div class="section" id="bond-style-harmonic-kk-command">
<h1>bond_style harmonic/kk command<a class="headerlink" href="#bond-style-harmonic-kk-command" title="Permalink to this headline"></a></h1> <h1>bond_style harmonic/kk command<a class="headerlink" href="#bond-style-harmonic-kk-command" title="Permalink to this headline"></a></h1>
</div> </div>

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doc/bond_harmonic.txt
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@ -7,6 +7,7 @@
:line :line
bond_style harmonic command :h3 bond_style harmonic command :h3
bond_style harmonic/intel command :h3
bond_style harmonic/kk command :h3 bond_style harmonic/kk command :h3
bond_style harmonic/omp command :h3 bond_style harmonic/omp command :h3

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doc/dihedral_charmm.html
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@ -127,6 +127,9 @@
<div class="section" id="dihedral-style-charmm-command"> <div class="section" id="dihedral-style-charmm-command">
<span id="index-0"></span><h1>dihedral_style charmm command<a class="headerlink" href="#dihedral-style-charmm-command" title="Permalink to this headline"></a></h1> <span id="index-0"></span><h1>dihedral_style charmm command<a class="headerlink" href="#dihedral-style-charmm-command" title="Permalink to this headline"></a></h1>
</div> </div>
<div class="section" id="dihedral-style-charmm-intel-command">
<h1>dihedral_style charmm/intel command<a class="headerlink" href="#dihedral-style-charmm-intel-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="dihedral-style-charmm-kk-command"> <div class="section" id="dihedral-style-charmm-kk-command">
<h1>dihedral_style charmm/kk command<a class="headerlink" href="#dihedral-style-charmm-kk-command" title="Permalink to this headline"></a></h1> <h1>dihedral_style charmm/kk command<a class="headerlink" href="#dihedral-style-charmm-kk-command" title="Permalink to this headline"></a></h1>
</div> </div>
@ -149,9 +152,9 @@ dihedral_coeff 1 120.0 1 60 0.5
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2> <h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>charmm</em> dihedral style uses the potential</p> <p>The <em>charmm</em> dihedral style uses the potential</p>
<img alt="_images/dihedral_charmm.jpg" class="align-center" src="_images/dihedral_charmm.jpg" /> <img alt="_images/dihedral_charmm.jpg" class="align-center" src="_images/dihedral_charmm.jpg" />
<p>See <a class="reference internal" href="special_bonds.html#mackerell"><span>(MacKerell)</span></a> for a description of the CHARMM force <p>See <a class="reference internal" href="#mackerell"><span>(MacKerell)</span></a> for a description of the CHARMM force
field. This dihedral style can also be used for the AMBER force field field. This dihedral style can also be used for the AMBER force field
(see comment on weighting factors below). See <a class="reference internal" href="special_bonds.html#cornell"><span>(Cornell)</span></a> (see comment on weighting factors below). See <a class="reference internal" href="#cornell"><span>(Cornell)</span></a>
for a description of the AMBER force field.</p> for a description of the AMBER force field.</p>
<p>The following coefficients must be defined for each dihedral type via the <p>The following coefficients must be defined for each dihedral type via the
<a class="reference internal" href="dihedral_coeff.html"><em>dihedral_coeff</em></a> command as in the example above, or in <a class="reference internal" href="dihedral_coeff.html"><em>dihedral_coeff</em></a> command as in the example above, or in

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doc/dihedral_charmm.txt
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:line :line
dihedral_style charmm command :h3 dihedral_style charmm command :h3
dihedral_style charmm/intel command :h3
dihedral_style charmm/kk command :h3 dihedral_style charmm/kk command :h3
dihedral_style charmm/omp command :h3 dihedral_style charmm/omp command :h3

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doc/improper_harmonic.html
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@ -127,6 +127,9 @@
<div class="section" id="improper-style-harmonic-command"> <div class="section" id="improper-style-harmonic-command">
<span id="index-0"></span><h1>improper_style harmonic command<a class="headerlink" href="#improper-style-harmonic-command" title="Permalink to this headline"></a></h1> <span id="index-0"></span><h1>improper_style harmonic command<a class="headerlink" href="#improper-style-harmonic-command" title="Permalink to this headline"></a></h1>
</div> </div>
<div class="section" id="improper-style-harmonic-intel-command">
<h1>improper_style harmonic/intel command<a class="headerlink" href="#improper-style-harmonic-intel-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="improper-style-harmonic-kk-command"> <div class="section" id="improper-style-harmonic-kk-command">
<h1>improper_style harmonic/kk command<a class="headerlink" href="#improper-style-harmonic-kk-command" title="Permalink to this headline"></a></h1> <h1>improper_style harmonic/kk command<a class="headerlink" href="#improper-style-harmonic-kk-command" title="Permalink to this headline"></a></h1>
</div> </div>

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doc/improper_harmonic.txt
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:line :line
improper_style harmonic command :h3 improper_style harmonic command :h3
improper_style harmonic/intel command :h3
improper_style harmonic/kk command :h3 improper_style harmonic/kk command :h3
improper_style harmonic/omp command :h3 improper_style harmonic/omp command :h3

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doc/searchindex.js
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