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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>
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<div class="section" id="ndx2group-command">
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<h1>ndx2group command<a class="headerlink" href="#ndx2group-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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ndx2group 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 or read in</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>
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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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ndx2group someindex.ndx
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ndx2group someindex.ndx 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 or read a Gromacs style index file in text format that associates
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atom IDs with the corresponding group definitions. This index file can be
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used 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. It can
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also be used to save and restore group definitions for static groups.</p>
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<p>The <em>group2ndx</em> command will write group definitions to an index file.
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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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<p>The <em>ndx2group</em> command will create of update group definitions from those
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stored in an index file. Without specifying any group IDs, all groups except
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<em>System</em> will be read from the index file and the corresponding groups
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recreated. If a group of the same name already exists, it will be completely
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reset. When specifying group IDs, those groups, if present, will be read
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from the index file and restored.</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 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>These commands are part of the USER-COLVARS package. They are only
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enabled if 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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