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<li>dihedral_style charmm command</li>
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<div class="section" id="dihedral-style-charmm-command">
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<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>
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</div>
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<div class="section" id="dihedral-style-charmm-intel-command">
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<h1>dihedral_style charmm/intel command<a class="headerlink" href="#dihedral-style-charmm-intel-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="dihedral-style-charmm-kk-command">
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<h1>dihedral_style charmm/kk command<a class="headerlink" href="#dihedral-style-charmm-kk-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="dihedral-style-charmm-omp-command">
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<h1>dihedral_style charmm/omp command<a class="headerlink" href="#dihedral-style-charmm-omp-command" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>dihedral_style charmm
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</pre></div>
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</div>
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</div>
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<div class="section" id="examples">
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<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>dihedral_style charmm
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dihedral_coeff 1 120.0 1 60 0.5
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</pre></div>
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</div>
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</div>
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<div class="section" id="description">
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<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
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<p>The <em>charmm</em> dihedral style uses the potential</p>
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<img alt="_images/dihedral_charmm.jpg" class="align-center" src="_images/dihedral_charmm.jpg" />
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<p>See <a class="reference internal" href="special_bonds.html#mackerell"><span>(MacKerell)</span></a> for a description of the CHARMM force
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field. This dihedral style can also be used for the AMBER force field
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(see comment on weighting factors below). See <a class="reference internal" href="special_bonds.html#cornell"><span>(Cornell)</span></a>
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for a description of the AMBER force field.</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"><em>dihedral_coeff</em></a> command as in the example above, or in
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the data file or restart files read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
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or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands:</p>
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<ul class="simple">
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<li>K (energy)</li>
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<li>n (integer >= 0)</li>
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<li>d (integer value of degrees)</li>
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<li>weighting factor (0.0 to 1.0)</li>
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</ul>
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<p>The weighting factor is applied to pairwise interaction between the
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1st and 4th atoms in the dihedral, which are computed by a CHARMM
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<a class="reference internal" href="pair_charmm.html"><em>pair_style</em></a> with epsilon and sigma values specified
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with a <a class="reference internal" href="pair_charmm.html"><em>pair_coeff</em></a> command. Note that this
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weighting factor is unrelated to the weighting factor specified by the
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<a class="reference internal" href="special_bonds.html"><em>special bonds</em></a> command which applies to all 1-4
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interactions in the system.</p>
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<p>For CHARMM force fields, the special_bonds 1-4 weighting factor should
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be set to 0.0. This is because the pair styles that contain “charmm”
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(e.g. <a class="reference internal" href="pair_charmm.html"><em>pair_style lj/charmm/coul/long</em></a>) define extra
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1-4 interaction coefficients that are used by this dihedral style to
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compute those interactions explicitly. This means that if any of the
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weighting factors defined as dihedral coefficients (4th coeff above)
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are non-zero, then you must use a charmm pair style. Note that if you
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do not set the special_bonds 1-4 weighting factor to 0.0 (which is the
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default) then 1-4 interactions in dihedrals will be computed twice,
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once by the pair routine and once by the dihedral routine, which is
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probably not what you want.</p>
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<p>For AMBER force fields, the special_bonds 1-4 weighting factor should
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be set to the AMBER defaults (1/2 and 5/6) and all the dihedral
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weighting factors (4th coeff above) should be set to 0.0. In this
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case, you can use any pair style you wish, since the dihedral does not
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need any 1-4 information.</p>
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<hr class="docutils" />
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<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
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functionally the same as the corresponding style without the suffix.
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They have been optimized to run faster, depending on your available
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hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
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of the manual. The accelerated styles take the same arguments and
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should produce the same results, except for round-off and precision
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issues.</p>
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<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
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KOKKOS, USER-OMP and OPT packages, respectively. They are only
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enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
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<p>You can specify the accelerated styles explicitly in your input script
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by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
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use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
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<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
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more instructions on how to use the accelerated styles effectively.</p>
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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<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
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<p>This dihedral style can only be used if LAMMPS was built with the
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MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info on packages.</p>
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</div>
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<div class="section" id="related-commands">
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<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
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<p><a class="reference internal" href="dihedral_coeff.html"><em>dihedral_coeff</em></a></p>
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<p><strong>Default:</strong> none</p>
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<hr class="docutils" />
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<p id="cornell"><strong>(Cornell)</strong> Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
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Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).</p>
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<p id="mackerell"><strong>(MacKerell)</strong> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
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Fischer, Gao, Guo, Ha, et al, J Phys Chem B, 102, 3586 (1998).</p>
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