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<title>group2ndx command — LAMMPS 15 May 2015 version documentation</title>
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<li>group2ndx command</li>
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<div class="section" id="group2ndx-command">
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<span id="index-0"></span><h1>group2ndx command<a class="headerlink" href="#group2ndx-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>group2ndx file group-ID ...
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</pre></div>
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</div>
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<ul class="simple">
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<li>file = name of index file to write out</li>
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<li>zero or more group IDs may be appended</li>
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</ul>
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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>group2ndx allindex.ndx
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group2ndx someindex.ndx upper lower mobile
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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>Write a Gromacs style index file in text format that associates atom IDs
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with the corresponding group definitions. This index file can be used
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with in combination with Gromacs analysis tools or to import group
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definitions into the <a class="reference internal" href="fix_colvars.html"><em>fix colvars</em></a> input file.</p>
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<p>Without specifying any group IDs, all groups will be written to the index
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file. When specifying group IDs, only those groups will be written to the
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index file. In order to follow the Gromacs conventions, the group <em>all</em>
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will be renamed to <em>System</em> in the index file.</p>
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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 command requires that atoms have atom IDs, since this is the
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information that is written to the index file.</p>
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<p>This fix is part of the USER-COLVARS package. It is only enabled if
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LAMMPS was built with that package. 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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</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="group.html"><em>group</em></a>, <a class="reference internal" href="dump.html"><em>dump</em></a>, <a class="reference internal" href="fix_colvars.html"><em>fix colvars</em></a></p>
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<p><strong>Default:</strong> none</p>
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