forked from lijiext/lammps
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384 lines
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<li class="toctree-l2"><a class="reference internal" href="dihedral_charmm.html">dihedral_style charmm command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_charmm.html#dihedral-style-charmm-intel-command">dihedral_style charmm/intel command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_charmm.html#dihedral-style-charmm-kk-command">dihedral_style charmm/kk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_charmm.html#dihedral-style-charmm-omp-command">dihedral_style charmm/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_class2.html">dihedral_style class2 command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_class2.html#dihedral-style-class2-omp-command">dihedral_style class2/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_cosine_shift_exp.html">dihedral_style cosine/shift/exp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_cosine_shift_exp.html#dihedral-style-cosine-shift-exp-omp-command">dihedral_style cosine/shift/exp/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_fourier.html">dihedral_style fourier command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_fourier.html#dihedral-style-fourier-omp-command">dihedral_style fourier/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_harmonic.html">dihedral_style harmonic command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_harmonic.html#dihedral-style-harmonic-intel-command">dihedral_style harmonic/intel command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_harmonic.html#dihedral-style-harmonic-omp-command">dihedral_style harmonic/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_helix.html">dihedral_style helix command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_helix.html#dihedral-style-helix-omp-command">dihedral_style helix/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_hybrid.html">dihedral_style hybrid command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_multi_harmonic.html">dihedral_style multi/harmonic command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_multi_harmonic.html#dihedral-style-multi-harmonic-omp-command">dihedral_style multi/harmonic/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_nharmonic.html">dihedral_style nharmonic command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_nharmonic.html#dihedral-style-nharmonic-omp-command">dihedral_style nharmonic/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_none.html">dihedral_style none command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_opls.html">dihedral_style opls command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_opls.html#dihedral-style-opls-intel-command">dihedral_style opls/intel command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_opls.html#dihedral-style-opls-kk-command">dihedral_style opls/kk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_opls.html#dihedral-style-opls-omp-command">dihedral_style opls/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_quadratic.html">dihedral_style quadratic command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_quadratic.html#dihedral-style-quadratic-omp-command">dihedral_style quadratic/omp command</a></li>
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<li class="toctree-l2 current"><a class="current reference internal" href="#">dihedral_style spherical command</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="#syntax">Syntax</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#examples">Examples</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#description">Description</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#restrictions">Restrictions</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#related-commands">Related commands</a></li>
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</ul>
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</li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_table.html">dihedral_style table command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_table.html#dihedral-style-table-omp-command">dihedral_style table/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_zero.html">dihedral_style zero command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_charmm.html">dihedral_style charmm command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_charmm.html#dihedral-style-charmm-intel-command">dihedral_style charmm/intel command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_charmm.html#dihedral-style-charmm-kk-command">dihedral_style charmm/kk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_charmm.html#dihedral-style-charmm-omp-command">dihedral_style charmm/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_class2.html">dihedral_style class2 command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_class2.html#dihedral-style-class2-omp-command">dihedral_style class2/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_cosine_shift_exp.html">dihedral_style cosine/shift/exp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_cosine_shift_exp.html#dihedral-style-cosine-shift-exp-omp-command">dihedral_style cosine/shift/exp/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_fourier.html">dihedral_style fourier command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_fourier.html#dihedral-style-fourier-omp-command">dihedral_style fourier/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_harmonic.html">dihedral_style harmonic command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_harmonic.html#dihedral-style-harmonic-intel-command">dihedral_style harmonic/intel command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_harmonic.html#dihedral-style-harmonic-omp-command">dihedral_style harmonic/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_helix.html">dihedral_style helix command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_helix.html#dihedral-style-helix-omp-command">dihedral_style helix/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_hybrid.html">dihedral_style hybrid command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_multi_harmonic.html">dihedral_style multi/harmonic command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_multi_harmonic.html#dihedral-style-multi-harmonic-omp-command">dihedral_style multi/harmonic/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_nharmonic.html">dihedral_style nharmonic command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_nharmonic.html#dihedral-style-nharmonic-omp-command">dihedral_style nharmonic/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_none.html">dihedral_style none command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_opls.html">dihedral_style opls command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_opls.html#dihedral-style-opls-intel-command">dihedral_style opls/intel command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_opls.html#dihedral-style-opls-kk-command">dihedral_style opls/kk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_opls.html#dihedral-style-opls-omp-command">dihedral_style opls/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_quadratic.html">dihedral_style quadratic command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_quadratic.html#dihedral-style-quadratic-omp-command">dihedral_style quadratic/omp command</a></li>
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<li class="toctree-l2 current"><a class="current reference internal" href="#">dihedral_style spherical command</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="#syntax">Syntax</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#examples">Examples</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#description">Description</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#restrictions">Restrictions</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#related-commands">Related commands</a></li>
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</ul>
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</li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_table.html">dihedral_style table command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_table.html#dihedral-style-table-omp-command">dihedral_style table/omp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_zero.html">dihedral_style zero command</a></li>
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<li>dihedral_style spherical command</li>
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<div class="section" id="dihedral-style-spherical-command">
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<span id="index-0"></span><h1>dihedral_style spherical command</h1>
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<div class="section" id="syntax">
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<h2>Syntax</h2>
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<pre class="literal-block">
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dihedral_style spherical
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</pre>
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</div>
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<div class="section" id="examples">
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<h2>Examples</h2>
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<pre class="literal-block">
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dihedral_coeff 1 1 286.1 1 124 1 1 90.0 0 1 90.0 0
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dihedral_coeff 1 3 286.1 1 114 1 1 90 0 1 90.0 0 &
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17.3 0 0.0 0 1 158 1 0 0.0 0 &
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15.1 0 0.0 0 0 0.0 0 1 167.3 1
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</pre>
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</div>
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<div class="section" id="description">
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<h2>Description</h2>
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<p>The <em>spherical</em> dihedral style uses the potential:</p>
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<img alt="_images/dihedral_spherical_angles.jpg" class="align-center" src="_images/dihedral_spherical_angles.jpg" />
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<img alt="_images/dihedral_spherical.jpg" class="align-center" src="_images/dihedral_spherical.jpg" />
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<p>For this dihedral style, the energy can be any function that combines the
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4-body dihedral-angle (phi) and the two 3-body bond-angles (theta1, theta2).
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For this reason, there is usually no need to define 3-body “angle” forces
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separately for the atoms participating in these interactions.
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It is probably more efficient to incorporate 3-body angle forces into
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the dihedral interaction even if it requires adding additional terms to
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the expansion (as was done in the second example). A careful choice of
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parameters can prevent singularities that occur with traditional
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force-fields whenever theta1 or theta2 approach 0 or 180 degrees.
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The last example above corresponds to an interaction with a single energy
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minima located at phi=114, theta1=158, theta2=167.3 degrees, and it remains
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numerically stable at all angles (phi, theta1, theta2). In this example,
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the coefficients 17.3, and 15.1 can be physically interpreted as the
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harmonic spring constants for theta1 and theta2 around their minima.
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The coefficient 286.1 is the harmonic spring constant for phi after
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division by sin(158)*sin(167.3) (the minima positions for theta1 and theta2).</p>
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<p>The following coefficients must be defined for each dihedral type via the
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<a class="reference internal" href="dihedral_coeff.html"><span class="doc">dihedral_coeff</span></a> command as in the example above, or in
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the Dihedral Coeffs section of a data file file read by the
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<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command:</p>
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<ul class="simple">
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<li>n (integer >= 1)</li>
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<li>C1 (energy)</li>
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<li>K1 (typically an integer)</li>
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<li>a1 (degrees)</li>
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<li>u1 (typically 0.0 or 1.0)</li>
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<li>L1 (typically an integer)</li>
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<li>b1 (degrees, typically 0.0 or 90.0)</li>
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<li>v1 (typically 0.0 or 1.0)</li>
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<li>M1 (typically an integer)</li>
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<li>c1 (degrees, typically 0.0 or 90.0)</li>
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<li>w1 (typically 0.0 or 1.0)</li>
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<li>[...]</li>
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<li>Cn (energy)</li>
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<li>Kn (typically an integer)</li>
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<li>an (degrees)</li>
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<li>un (typically 0.0 or 1.0)</li>
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<li>Ln (typically an integer)</li>
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<li>bn (degrees, typically 0.0 or 90.0)</li>
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<li>vn (typically 0.0 or 1.0)</li>
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<li>Mn (typically an integer)</li>
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<li>cn (degrees, typically 0.0 or 90.0)</li>
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<li>wn (typically 0.0 or 1.0)</li>
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</ul>
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</div>
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<hr class="docutils" />
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<div class="section" id="restrictions">
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<h2>Restrictions</h2>
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<p>This dihedral style can only be used if LAMMPS was built with the
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USER_MISC package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a>
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section for more info on packages.</p>
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<div class="section" id="related-commands">
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<h2>Related commands</h2>
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<p><a class="reference internal" href="dihedral_coeff.html"><span class="doc">dihedral_coeff</span></a></p>
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<p><strong>Default:</strong> none</p>
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