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<li><a class="reference internal" href="#">fix spring/chunk command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
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<div class="section" id="fix-spring-chunk-command">
<span id="index-0"></span><h1>fix spring/chunk command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">spring</span><span class="o">/</span><span class="n">chunk</span> <span class="n">K</span> <span class="n">chunkID</span> <span class="n">comID</span>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>spring/chunk = style name of this fix command</li>
<li>K = spring constant for each chunk (force/distance units)</li>
<li>chunkID = ID of <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command</li>
<li>comID = ID of <a class="reference internal" href="compute_com_chunk.html"><span class="doc">compute com/chunk</span></a> command</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">restrain</span> <span class="nb">all</span> <span class="n">spring</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">100</span> <span class="n">chunkID</span> <span class="n">comID</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Apply a spring force to the center-of-mass (COM) of chunks of atoms as
defined by the <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command.
Chunks can be molecules or spatial bins or other groupings of atoms.
This is a way of tethering each chunk to its initial COM coordinates.</p>
<p>The <em>chunkID</em> is the ID of a compute chunk/atom command defined in the
input script. It is used to define the chunks. The <em>comID</em> is the ID
of a compute com/chunk command defined in the input script. It is
used to compute the COMs of each chunk.</p>
<p>At the beginning of the first <a class="reference internal" href="run.html"><span class="doc">run</span></a> or
<a class="reference internal" href="minimize.html"><span class="doc">minimize</span></a> command after this fix is defined, the
initial COM of each chunk is calculated and stored as R0m, where M is
the chunk number. Thereafter, at every timestep (or minimization
iteration), the current COM of each chunk is calculated as Rm. A
restoring force of magnitude K (Rm - R0m) Mi / Mm is applied to each
atom in each chunk where <em>K</em> is the specified spring constant, Mi is
the mass of the atom, and Mm is the total mass of all atoms in the
chunk. Note that <em>K</em> thus represents the spring constant for the
total force on each chunk of atoms, not for a spring applied to each
atom.</p>
</div>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
fix to add the energy stored in all the springs to the system&#8217;s potential
energy as part of <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a>.</p>
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>respa</em> option is supported by this
fix. This allows to set at which level of the <a class="reference internal" href="run_style.html"><span class="doc">r-RESPA</span></a>
integrator the fix is adding its forces. Default is the outermost level.</p>
<p>This fix computes a global scalar which can be accessed by various
<a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. The scalar is the
energy of all the springs, i.e. 0.5 * K * r^2 per-spring.</p>
<p>The scalar value calculated by this fix is &#8220;extensive&#8221;.</p>
<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command.</p>
<p>The forces due to this fix are imposed during an energy minimization,
invoked by the <a class="reference internal" href="minimize.html"><span class="doc">minimize</span></a> command.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">If you want the spring energies to be included in the total
potential energy of the system (the quantity being minimized), you
MUST enable the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option for this
fix.</p>
</div>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<blockquote>
<div>none</div></blockquote>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="fix_spring.html"><span class="doc">fix spring</span></a>, <a class="reference internal" href="fix_spring_self.html"><span class="doc">fix spring/self</span></a>,
<a class="reference internal" href="fix_spring_rg.html"><span class="doc">fix spring/rg</span></a></p>
<p><strong>Default:</strong> none</p>
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